Today, I had a case that only “some files” weren’t visible inside a vault on iCloud Drive. The reason was that iCloud Drive isn’t as transparent as we thought. If the files are not available offline, Cryptomator is unable to see them.
After pressing the “download from cloud” icon, the content was available offline. After that, I was able to see all my files again.
You could also disable this setting in System Preferences → Apple ID → iCloud.
