Sorry this is a long post.
The last time I had a similar problem, it occurred during a cryptomator upgrade. And the answer at that time was that I needed to install libfuse3. Link as follows
This time I started out (in Debian 12 container) with fuse3 already installed, but the cryptomator appimage wouldn’t even launch to the GUI with those. (It didn’t launch to the GUI until I added the fuse2 stuff, and at that point I could get in and verify that it was using fuse rather than webdav, but it couldn’t see my file system).