Michael:
Now it gets weird.
I closed the vault to make a backup of my log files for further investigation.
Then I opened the vault again because I wanted to know what is the content of the file in the vault that is actually shown by WinMerge as a different file. I wanted to know: which file is “right” and which is “wrong” in the vault.
I navigated to the directory of the affected files (both of them), and found every file 100% correct in the vault.
No mismatch between filename and content, everything is ok, nothing missing.
I was very confused, so I refreshed the same WinMerge comparison (completely) and: no differences anymore.
I checked the log files but I cannot see anything that explained this. (and there are many, many times the affected file is named in the log)
I closed Cryptomator, moved all the existing log files away, started Cryptomator, opened only one vault, and ran the comparison again (completely).
Surprisingly I had again a missmacht report by WinMerge, but with a complete different file (I’m also sure I havent touched id).
This is a vague hint (confirmed on GitHub ) that the ciphertext files are all intact and the problem only occurs when showing the decrypted view. Which isn’t exactly good but still kind of comforting. Probably some issue with cleartext blocks cached in memory.