I have iCloud set to Optimize Storage (so that the OS will offload local files as needed for space). This has never been an issue in the past; if I’m browsing a Cryptomator vault, it will show the files and download them as needed to un-encrypt and open.
On M1 Macs, however, it seems like this now breaks Cryptomator and I can no longer reliably access files in the vault. Folders that haven’t been downloaded locally just show as empty when browsing an unlocked vault. I thought I had data loss issues, but accessing the same folders (not downloaded) via the iOS app shows the files and downloads as needed to un-encrypt and view.
Using the latest macFuse (4.2.3), Cryptomator (1.6.4), and macOS 12.0.1 (though the issue has persisted on macOS 11 on M1 Macs, as well).