Silent install while application is running corrupts install

[JayG30]

I'm testing silent upgrades of pdfsam through winget, which uses the msi installer.
I had version 5.1.1 open and running while winget finds and performs a silent upgrade to 5.1.2.

The result of this is that the current 5.1.1 version remains open, the 5.1.2 version appears to get installed and says that the system needs to be rebooted. Looking in the app/mods folder of the install directory there appears to be old and new versions of files. Closing the running version leaves you with an install that won't run. Performing a reboot cleans up a bunch of older versions of files in the install directory. However, application still fails. Running the .bat file says it's missing "jakarta.inject".

Is there any way to properly handle upgrades to the software silently in the background if the application is currently running?

If not I will have to script something to terminate the processes and hope a user doesn't try running it again before the upgrade kicks off.