diff --git a/README-CHANGES.xml b/README-CHANGES.xml
index b43acba..3f216dc 100644
--- a/README-CHANGES.xml
+++ b/README-CHANGES.xml
@@ -24,14 +24,28 @@
         <c:change date="2020-12-19T00:00:00+00:00" summary="Slightly improve the CSS for table elements"/>
       </c:changes>
     </c:release>
-    <c:release date="2021-06-27T16:34:56+00:00" is-open="true" ticket-system="com.github.io7m.xstructural" version="1.3.0">
+    <c:release date="2022-02-03T00:00:00+00:00" is-open="false" ticket-system="com.github.io7m.xstructural" version="1.3.0">
       <c:changes>
         <c:change date="2021-06-27T00:00:00+00:00" summary="Add EPUB support">
           <c:tickets>
             <c:ticket id="13"/>
           </c:tickets>
         </c:change>
-        <c:change date="2021-06-27T16:34:56+00:00" summary="Fix a schema bug that rejected valid footnotes in documents"/>
+        <c:change date="2021-06-27T00:00:00+00:00" summary="Fix a schema bug that rejected valid footnotes in documents"/>
+      </c:changes>
+    </c:release>
+    <c:release date="2022-02-03T22:22:51+00:00" is-open="false" ticket-system="com.github.io7m.xstructural" version="1.4.0">
+      <c:changes>
+        <c:change date="2022-02-03T00:00:00+00:00" summary="Fix a bug where documents with comments would be rejected">
+          <c:tickets>
+            <c:ticket id="18"/>
+          </c:tickets>
+        </c:change>
+        <c:change date="2022-02-03T00:00:00+00:00" summary="Ensure existing files are replaced when producing EPUBs">
+          <c:tickets>
+            <c:ticket id="20"/>
+          </c:tickets>
+        </c:change>
       </c:changes>
     </c:release>
   </c:releases>
diff --git a/com.io7m.xstructural.api/pom.xml b/com.io7m.xstructural.api/pom.xml
index 52d10c7..927b242 100644
--- a/com.io7m.xstructural.api/pom.xml
+++ b/com.io7m.xstructural.api/pom.xml
@@ -9,7 +9,7 @@
   <parent>
     <artifactId>com.io7m.xstructural</artifactId>
     <groupId>com.io7m.xstructural</groupId>
-    <version>1.3.0</version>
+    <version>1.4.0</version>
   </parent>
 
   <artifactId>com.io7m.xstructural.api</artifactId>
diff --git a/com.io7m.xstructural.cmdline/pom.xml b/com.io7m.xstructural.cmdline/pom.xml
index f4cef1b..d4f8be3 100644
--- a/com.io7m.xstructural.cmdline/pom.xml
+++ b/com.io7m.xstructural.cmdline/pom.xml
@@ -9,7 +9,7 @@
   <parent>
     <artifactId>com.io7m.xstructural</artifactId>
     <groupId>com.io7m.xstructural</groupId>
-    <version>1.3.0</version>
+    <version>1.4.0</version>
   </parent>
 
   <artifactId>com.io7m.xstructural.cmdline</artifactId>
diff --git a/com.io7m.xstructural.documentation/pom.xml b/com.io7m.xstructural.documentation/pom.xml
index ac4538a..e160ec6 100644
--- a/com.io7m.xstructural.documentation/pom.xml
+++ b/com.io7m.xstructural.documentation/pom.xml
@@ -9,7 +9,7 @@
   <parent>
     <artifactId>com.io7m.xstructural</artifactId>
     <groupId>com.io7m.xstructural</groupId>
-    <version>1.3.0</version>
+    <version>1.4.0</version>
   </parent>
 
   <artifactId>com.io7m.xstructural.documentation</artifactId>
diff --git a/com.io7m.xstructural.tests/pom.xml b/com.io7m.xstructural.tests/pom.xml
index 0f1391e..dd5a7d5 100644
--- a/com.io7m.xstructural.tests/pom.xml
+++ b/com.io7m.xstructural.tests/pom.xml
@@ -8,7 +8,7 @@
   <parent>
     <artifactId>com.io7m.xstructural</artifactId>
     <groupId>com.io7m.xstructural</groupId>
-    <version>1.3.0</version>
+    <version>1.4.0</version>
   </parent>
 
   <artifactId>com.io7m.xstructural.tests</artifactId>
diff --git a/com.io7m.xstructural.tests/src/test/java/com/io7m/xstructural/tests/XSCommandLineTest.java b/com.io7m.xstructural.tests/src/test/java/com/io7m/xstructural/tests/XSCommandLineTest.java
index 912a5af..54ee4f1 100644
--- a/com.io7m.xstructural.tests/src/test/java/com/io7m/xstructural/tests/XSCommandLineTest.java
+++ b/com.io7m.xstructural.tests/src/test/java/com/io7m/xstructural/tests/XSCommandLineTest.java
@@ -991,4 +991,75 @@ public void testTransformXHTMLEPUBOKExample0_80()
       "EPUB file exists"
     );
   }
+
+  @Test
+  public void testTransformXHTMLEPUBOKExampleTwice_80()
+    throws Exception
+  {
+    XSTestDirectories.resourceOf(
+      XSCommandLineTest.class,
+      this.sourceDirectory,
+      "poppy.jpg"
+    );
+    XSTestDirectories.resourceOf(
+      XSCommandLineTest.class,
+      this.sourceDirectory,
+      "missing.jpg"
+    );
+    XSTestDirectories.resourceOf(
+      XSCommandLineTest.class,
+      this.sourceDirectory,
+      "woods.jpg"
+    );
+
+    {
+      final var main = new Main(new String[]{
+        "epub",
+        "--sourceFile",
+        XSTestDirectories.resourceOf(
+          XSCommandLineTest.class,
+          this.sourceDirectory,
+          "example0_80.xml")
+          .toString(),
+        "--outputDirectory",
+        this.outputDirectory.toString(),
+        "--traceFile",
+        this.directory.resolve("trace.xml").toString(),
+        "--messagesFile",
+        this.directory.resolve("messages.log").toString(),
+        "--verbose",
+        "trace"
+      });
+
+      final var capture =
+        XSOutputCaptured.capture(main::run);
+
+      Assertions.assertEquals(0, main.exitCode());
+    }
+
+    {
+      final var main = new Main(new String[]{
+        "epub",
+        "--sourceFile",
+        XSTestDirectories.resourceOf(
+          XSCommandLineTest.class,
+          this.sourceDirectory,
+          "example0_80.xml")
+          .toString(),
+        "--outputDirectory",
+        this.outputDirectory.toString(),
+        "--traceFile",
+        this.directory.resolve("trace.xml").toString(),
+        "--messagesFile",
+        this.directory.resolve("messages.log").toString(),
+        "--verbose",
+        "trace"
+      });
+
+      final var capture =
+        XSOutputCaptured.capture(main::run);
+
+      Assertions.assertEquals(0, main.exitCode());
+    }
+  }
 }
diff --git a/com.io7m.xstructural.tests/src/test/java/com/io7m/xstructural/tests/XSTestDirectories.java b/com.io7m.xstructural.tests/src/test/java/com/io7m/xstructural/tests/XSTestDirectories.java
index 5a5cc32..100c4c3 100644
--- a/com.io7m.xstructural.tests/src/test/java/com/io7m/xstructural/tests/XSTestDirectories.java
+++ b/com.io7m.xstructural.tests/src/test/java/com/io7m/xstructural/tests/XSTestDirectories.java
@@ -24,6 +24,7 @@
 import java.nio.file.Files;
 import java.nio.file.NoSuchFileException;
 import java.nio.file.Path;
+import java.nio.file.StandardCopyOption;
 import java.util.UUID;
 
 public final class XSTestDirectories
@@ -70,7 +71,7 @@ public static Path resourceOf(
     LOGGER.debug("copy {} {}", name, target);
 
     try (var stream = url.openStream()) {
-      Files.copy(stream, target);
+      Files.copy(stream, target, StandardCopyOption.REPLACE_EXISTING);
     }
     return target;
   }
diff --git a/com.io7m.xstructural.tests/src/test/resources/com/io7m/xstructural/tests/example0_70.xml b/com.io7m.xstructural.tests/src/test/resources/com/io7m/xstructural/tests/example0_70.xml
index fbbd347..122a9f0 100644
--- a/com.io7m.xstructural.tests/src/test/resources/com/io7m/xstructural/tests/example0_70.xml
+++ b/com.io7m.xstructural.tests/src/test/resources/com/io7m/xstructural/tests/example0_70.xml
@@ -1,10 +1,14 @@
 <?xml version="1.0" encoding="UTF-8" ?>
 
+<!-- Comments! -->
+
 <Document xmlns="urn:com.io7m.structural:7:0"
           xmlns:dc="http://purl.org/dc/elements/1.1/"
           tableOfContentsDepth="3"
           tableOfContents="true">
 
+  <!-- Comments! -->
+
   <Metadata>
     <dc:contributor>A Contributor</dc:contributor>
     <dc:creator>A Creator</dc:creator>
diff --git a/com.io7m.xstructural.tests/src/test/resources/com/io7m/xstructural/tests/example0_80.xml b/com.io7m.xstructural.tests/src/test/resources/com/io7m/xstructural/tests/example0_80.xml
index 3cb05a6..0f2fcb7 100644
--- a/com.io7m.xstructural.tests/src/test/resources/com/io7m/xstructural/tests/example0_80.xml
+++ b/com.io7m.xstructural.tests/src/test/resources/com/io7m/xstructural/tests/example0_80.xml
@@ -1,10 +1,14 @@
 <?xml version="1.0" encoding="UTF-8" ?>
 
+<!-- Comments! -->
+
 <Document xmlns="urn:com.io7m.structural:8:0"
           xmlns:dc="http://purl.org/dc/elements/1.1/"
           tableOfContentsDepth="3"
           tableOfContents="true">
 
+  <!-- Comments! -->
+
   <Metadata>
     <dc:contributor>A Contributor</dc:contributor>
     <dc:creator>A Creator</dc:creator>
diff --git a/com.io7m.xstructural.tests/src/test/resources/com/io7m/xstructural/tests/example1_70.xml b/com.io7m.xstructural.tests/src/test/resources/com/io7m/xstructural/tests/example1_70.xml
index 65432e3..40cff89 100644
--- a/com.io7m.xstructural.tests/src/test/resources/com/io7m/xstructural/tests/example1_70.xml
+++ b/com.io7m.xstructural.tests/src/test/resources/com/io7m/xstructural/tests/example1_70.xml
@@ -1,10 +1,14 @@
 <?xml version="1.0" encoding="UTF-8" ?>
 
+<!-- Comments! -->
+
 <Document xmlns="urn:com.io7m.structural:7:0"
           xmlns:dc="http://purl.org/dc/elements/1.1/"
           tableOfContentsDepth="3"
           tableOfContents="true">
 
+  <!-- Comments! -->
+
   <Metadata>
     <dc:contributor>A Contributor</dc:contributor>
     <dc:creator>A Creator</dc:creator>
diff --git a/com.io7m.xstructural.tests/src/test/resources/com/io7m/xstructural/tests/example1_80.xml b/com.io7m.xstructural.tests/src/test/resources/com/io7m/xstructural/tests/example1_80.xml
index 41c9cc8..6ff5332 100644
--- a/com.io7m.xstructural.tests/src/test/resources/com/io7m/xstructural/tests/example1_80.xml
+++ b/com.io7m.xstructural.tests/src/test/resources/com/io7m/xstructural/tests/example1_80.xml
@@ -1,10 +1,14 @@
 <?xml version="1.0" encoding="UTF-8" ?>
 
+<!-- Comments! -->
+
 <Document xmlns="urn:com.io7m.structural:8:0"
           xmlns:dc="http://purl.org/dc/elements/1.1/"
           tableOfContentsDepth="3"
           tableOfContents="true">
 
+  <!-- Comments! -->
+
   <Metadata>
     <dc:contributor>A Contributor</dc:contributor>
     <dc:creator>A Creator</dc:creator>
diff --git a/com.io7m.xstructural.tests/src/test/resources/com/io7m/xstructural/tests/example2_70.xml b/com.io7m.xstructural.tests/src/test/resources/com/io7m/xstructural/tests/example2_70.xml
index 316de3c..f6d8c1a 100644
--- a/com.io7m.xstructural.tests/src/test/resources/com/io7m/xstructural/tests/example2_70.xml
+++ b/com.io7m.xstructural.tests/src/test/resources/com/io7m/xstructural/tests/example2_70.xml
@@ -1,10 +1,14 @@
 <?xml version="1.0" encoding="UTF-8" ?>
 
+<!-- Comments! -->
+
 <Document xmlns="urn:com.io7m.structural:7:0"
           xmlns:dc="http://purl.org/dc/elements/1.1/"
           tableOfContentsDepth="3"
           tableOfContents="true">
 
+  <!-- Comments! -->
+
   <Metadata>
     <dc:contributor>A Contributor</dc:contributor>
     <dc:creator>A Creator</dc:creator>
diff --git a/com.io7m.xstructural.tests/src/test/resources/com/io7m/xstructural/tests/example2_80.xml b/com.io7m.xstructural.tests/src/test/resources/com/io7m/xstructural/tests/example2_80.xml
index 6f143ec..6d8adb0 100644
--- a/com.io7m.xstructural.tests/src/test/resources/com/io7m/xstructural/tests/example2_80.xml
+++ b/com.io7m.xstructural.tests/src/test/resources/com/io7m/xstructural/tests/example2_80.xml
@@ -1,10 +1,14 @@
 <?xml version="1.0" encoding="UTF-8" ?>
 
+<!-- Comments! -->
+
 <Document xmlns="urn:com.io7m.structural:8:0"
           xmlns:dc="http://purl.org/dc/elements/1.1/"
           tableOfContentsDepth="3"
           tableOfContents="true">
 
+  <!-- Comments! -->
+
   <Metadata>
     <dc:contributor>A Contributor</dc:contributor>
     <dc:creator>A Creator</dc:creator>
diff --git a/com.io7m.xstructural.tests/src/test/resources/com/io7m/xstructural/tests/example3_70.xml b/com.io7m.xstructural.tests/src/test/resources/com/io7m/xstructural/tests/example3_70.xml
index 69e95ac..dbd0b1d 100644
--- a/com.io7m.xstructural.tests/src/test/resources/com/io7m/xstructural/tests/example3_70.xml
+++ b/com.io7m.xstructural.tests/src/test/resources/com/io7m/xstructural/tests/example3_70.xml
@@ -1,10 +1,14 @@
 <?xml version="1.0" encoding="UTF-8" ?>
 
+<!-- Comments! -->
+
 <Document xmlns="urn:com.io7m.structural:7:0"
           xmlns:dc="http://purl.org/dc/elements/1.1/"
           tableOfContentsDepth="3"
           tableOfContents="true">
 
+  <!-- Comments! -->
+
   <Metadata>
     <dc:contributor>A Contributor</dc:contributor>
     <dc:creator>A Creator</dc:creator>
diff --git a/com.io7m.xstructural.tests/src/test/resources/com/io7m/xstructural/tests/example3_80.xml b/com.io7m.xstructural.tests/src/test/resources/com/io7m/xstructural/tests/example3_80.xml
index 2e81d78..cc6e954 100644
--- a/com.io7m.xstructural.tests/src/test/resources/com/io7m/xstructural/tests/example3_80.xml
+++ b/com.io7m.xstructural.tests/src/test/resources/com/io7m/xstructural/tests/example3_80.xml
@@ -1,10 +1,14 @@
 <?xml version="1.0" encoding="UTF-8" ?>
 
+<!-- Comments! -->
+
 <Document xmlns="urn:com.io7m.structural:8:0"
           xmlns:dc="http://purl.org/dc/elements/1.1/"
           tableOfContentsDepth="3"
           tableOfContents="true">
 
+  <!-- Comments! -->
+
   <Metadata>
     <dc:contributor>A Contributor</dc:contributor>
     <dc:creator>A Creator</dc:creator>
diff --git a/com.io7m.xstructural.vanilla/pom.xml b/com.io7m.xstructural.vanilla/pom.xml
index db010b1..a457872 100644
--- a/com.io7m.xstructural.vanilla/pom.xml
+++ b/com.io7m.xstructural.vanilla/pom.xml
@@ -9,7 +9,7 @@
   <parent>
     <artifactId>com.io7m.xstructural</artifactId>
     <groupId>com.io7m.xstructural</groupId>
-    <version>1.3.0</version>
+    <version>1.4.0</version>
   </parent>
 
   <artifactId>com.io7m.xstructural.vanilla</artifactId>
diff --git a/com.io7m.xstructural.vanilla/src/main/java/com/io7m/xstructural/vanilla/internal/XSEPUBCreator.java b/com.io7m.xstructural.vanilla/src/main/java/com/io7m/xstructural/vanilla/internal/XSEPUBCreator.java
index dd0ed8d..ce7c740 100644
--- a/com.io7m.xstructural.vanilla/src/main/java/com/io7m/xstructural/vanilla/internal/XSEPUBCreator.java
+++ b/com.io7m.xstructural.vanilla/src/main/java/com/io7m/xstructural/vanilla/internal/XSEPUBCreator.java
@@ -44,6 +44,10 @@
 import java.util.zip.ZipEntry;
 
 import static java.nio.charset.StandardCharsets.UTF_8;
+import static java.nio.file.StandardCopyOption.REPLACE_EXISTING;
+import static java.nio.file.StandardOpenOption.CREATE;
+import static java.nio.file.StandardOpenOption.TRUNCATE_EXISTING;
+import static java.nio.file.StandardOpenOption.WRITE;
 
 /**
  * An EPUB creator.
@@ -466,7 +470,7 @@ private void copyOEBPS()
           this.oebpsDirectory.resolve(file.getFileName().toString());
 
         LOG.info("copy {} {}", file, outputFile);
-        Files.copy(file, outputFile);
+        Files.copy(file, outputFile, REPLACE_EXISTING);
       }
     }
   }
@@ -488,7 +492,11 @@ private void writeContainerFile()
     throws IOException
   {
     try (var stream = resource("container.xml")) {
-      Files.copy(stream, this.metaDirectory.resolve("container.xml"));
+      Files.copy(
+        stream,
+        this.metaDirectory.resolve("container.xml"),
+        REPLACE_EXISTING
+      );
     }
   }
 
@@ -498,7 +506,10 @@ private void writeMimetypeFile()
     Files.writeString(
       this.epubDirectory.resolve("mimetype"),
       "application/epub+zip",
-      UTF_8
+      UTF_8,
+      WRITE,
+      CREATE,
+      TRUNCATE_EXISTING
     );
   }
 
diff --git a/com.io7m.xstructural.xml/pom.xml b/com.io7m.xstructural.xml/pom.xml
index e301e42..574fc9c 100644
--- a/com.io7m.xstructural.xml/pom.xml
+++ b/com.io7m.xstructural.xml/pom.xml
@@ -6,7 +6,7 @@
   <parent>
     <groupId>com.io7m.xstructural</groupId>
     <artifactId>com.io7m.xstructural</artifactId>
-    <version>1.3.0</version>
+    <version>1.4.0</version>
   </parent>
 
   <artifactId>com.io7m.xstructural.xml</artifactId>
diff --git a/com.io7m.xstructural.xml/src/main/xsl/com/io7m/xstructural/xml/s7/xstructural7-web-multi.xsl b/com.io7m.xstructural.xml/src/main/xsl/com/io7m/xstructural/xml/s7/xstructural7-web-multi.xsl
index 949e363..ce9af1b 100644
--- a/com.io7m.xstructural.xml/src/main/xsl/com/io7m/xstructural/xml/s7/xstructural7-web-multi.xsl
+++ b/com.io7m.xstructural.xml/src/main/xsl/com/io7m/xstructural/xml/s7/xstructural7-web-multi.xsl
@@ -37,6 +37,8 @@
                  select="concat('Unexpectedly reached catch-all template: ', namespace-uri(.), ':',  node-name(.))"/>
   </xsl:template>
 
+  <xsl:template match="comment()"/>
+
   <!--                                -->
   <!-- Top-level web multi templates. -->
   <!--                                -->
diff --git a/com.io7m.xstructural.xml/src/main/xsl/com/io7m/xstructural/xml/s7/xstructural7-web-single.xsl b/com.io7m.xstructural.xml/src/main/xsl/com/io7m/xstructural/xml/s7/xstructural7-web-single.xsl
index 0798ea6..96095d7 100644
--- a/com.io7m.xstructural.xml/src/main/xsl/com/io7m/xstructural/xml/s7/xstructural7-web-single.xsl
+++ b/com.io7m.xstructural.xml/src/main/xsl/com/io7m/xstructural/xml/s7/xstructural7-web-single.xsl
@@ -36,6 +36,8 @@
                  select="concat('Unexpectedly reached catch-all template: ', namespace-uri(.), ':',  node-name(.))"/>
   </xsl:template>
 
+  <xsl:template match="comment()"/>
+
   <!--                                 -->
   <!-- Top-level web single templates. -->
   <!--                                 -->
diff --git a/com.io7m.xstructural.xml/src/main/xsl/com/io7m/xstructural/xml/s8/xstructural8-web-multi.xsl b/com.io7m.xstructural.xml/src/main/xsl/com/io7m/xstructural/xml/s8/xstructural8-web-multi.xsl
index f702b98..3e260c0 100644
--- a/com.io7m.xstructural.xml/src/main/xsl/com/io7m/xstructural/xml/s8/xstructural8-web-multi.xsl
+++ b/com.io7m.xstructural.xml/src/main/xsl/com/io7m/xstructural/xml/s8/xstructural8-web-multi.xsl
@@ -37,6 +37,8 @@
                  select="concat('Unexpectedly reached catch-all template: ', namespace-uri(.), ':',  node-name(.))"/>
   </xsl:template>
 
+  <xsl:template match="comment()"/>
+
   <!--                                -->
   <!-- Top-level web multi templates. -->
   <!--                                -->
diff --git a/com.io7m.xstructural.xml/src/main/xsl/com/io7m/xstructural/xml/s8/xstructural8-web-single.xsl b/com.io7m.xstructural.xml/src/main/xsl/com/io7m/xstructural/xml/s8/xstructural8-web-single.xsl
index a880400..8f6af26 100644
--- a/com.io7m.xstructural.xml/src/main/xsl/com/io7m/xstructural/xml/s8/xstructural8-web-single.xsl
+++ b/com.io7m.xstructural.xml/src/main/xsl/com/io7m/xstructural/xml/s8/xstructural8-web-single.xsl
@@ -36,6 +36,8 @@
                  select="concat('Unexpectedly reached catch-all template: ', namespace-uri(.), ':',  node-name(.))"/>
   </xsl:template>
 
+  <xsl:template match="comment()"/>
+
   <!--                                 -->
   <!-- Top-level web single templates. -->
   <!--                                 -->
diff --git a/pom.xml b/pom.xml
index c097406..e01b6af 100644
--- a/pom.xml
+++ b/pom.xml
@@ -11,7 +11,7 @@
 
   <groupId>com.io7m.xstructural</groupId>
   <artifactId>com.io7m.xstructural</artifactId>
-  <version>1.3.0</version>
+  <version>1.4.0</version>
   <packaging>pom</packaging>
 
   <description>Structural document format</description>
@@ -29,7 +29,7 @@
 
   <properties>
     <com.io7m.immutables.version>2.8.8</com.io7m.immutables.version>
-    <io7m.api.previousVersion>1.2.0</io7m.api.previousVersion>
+    <io7m.api.previousVersion>1.3.0</io7m.api.previousVersion>
     <junit.version>5.7.0</junit.version>
   </properties>