I use cryptomator on Mac and windows. It turns out that on Mac the folders and files are displayed normally while in Windows some folders are empty.
I have already updated to the latest version and it still does not work.
I noticed that on Mac if I switch from FUSE to Webdav almost no folder is displayed.
Have a similar problem. In my case it was related to too long path names and only occured in Dokany mode.
Try this to confirm: Shorten the path name of the empty folder (just try changing the longest one or two folder names into one letter names temporarily). Do the files re-appear?
You can also try mounting Cryptomator in Dokany mode (unmount the drive, click the settings gear on the bottom and chose Dokany instead of WebDAV, then mount the drive again). In Dokany mode my files are listed even with long path names.
This is highly irritating. Of course we cannot find the files, but even more critically, it is easy to accidentally delete folders that seem empty and in fact still contain data!
The reason why I am still using WebDAV is that Dokany for some strange reason performs EXTREMELY slow on my machine. Still figuring out why.