.emDB project changes lost after saving, closing then reloading

[SamDeCraemer]

Describe the bug
Sometimes an .EMDB project file I’m working on no longer updates its bookmark table (nor anything else as far as I can see) when changing then saving. If I close then reopen the project, the bookmark table reflects an earlier save no matter how many times I try to edit and save again. The problem is that I have no indication when this starts to happen, causing me to lose progress from time to time, sometimes a lot.
I have isolated a file now that has this issue, and can try any suggestions you might have to try to pin down the problem, or send the files.

To Reproduce
This happens infrequently, I have not been able to identify exactly how to reproduce it. I do open other .emdb files sometimes to check things while working mostly on one project, but this doesn’t always cause troubles. See additional context for some things that do or do not help to circumvent the issue once it starts

Expected behavior
I expect saving a .emdb file to always save the bookmark table in its current state, without having to change the file name

Screenshots
Not applicable

System (please complete the following information):

• OS: Windows 10
• Version v0.12.0

Additional context
Saving the emdb file under a different name does include the update. Every save from that point on requires me to change the name again.

The action below did not solve the problem (changes made were lost after saving then closing and reopening):
• Restarting the pc then trying again to update then save the bookmark table in the same project
• Copy the emdb file and all related mzml files to a different drive on the same pc, and remove the mzml files from the original location to force El-Maven to (succesfully) find the files in their new location, then modifying the bookmark table and saving the .emdb file under the same name.
• Copy the emdb file and all related mzml files to a different pc, open, modify table then save without changing the name.

Best regards,
Sam

[bifidotftw]

I have the same system and I always run into this problem when I edit saved .emdb files and save them again.

Works:
Open maven, load files, mark peaks in library, save

Does not work:
Open .emdb file, mark peaks in library, save

I always have two El-Maven instances of the same .mzML files open (negative & positive mode).

I work with large data sets, therefore my memory is usually at it's limit and my computer is running quite slow, which is why I occasionally get the following error messages:

Possibly small freezes, e.g. when memory is being swapped, could cause the problem.