I use Cryptomator on Windows, Linux, and Android with data stored in a hosted Nextcloud instance.
Some time ago, I had problems renaming files or subdirectories, but I was able to work around and solve them all somehow. However, yesterday, for the first time, two files disappeared without a trace after I performed the following steps in quick succession on Windows:
a) changed the name of the .odt file
b) changed the name of the subdirectory where this file is located, and
c) mistakenly moved the file to a deeper subdirectory containing older versions.
d) moved the file back to its previous directory.
The file that was moved back and forth was displayed normally in the file system.
When I tried to open this file by double-clicking on it, an error message appeared stating that the file did not exist.
After that, it was no longer displayed in the file system. I suspect that renaming files and subdirectories can cause problems that are difficult or impossible to trace and solve. See also:
Problem with moved files disappearing on Linux side.
In future, I should be careful when renaming files in a vault and, just in case, create a copy of the file or directory in a local directory on my PC before changing the name.