The current version of Google Drive file stream has a bug where it will randomly stop exposing several subfolders for a user’s account on a desktop’s drive (Files/Folders Missing from Finder when using Google Drive FS on macOS - Google Drive Community). The only fix I know of for this is to disconnect the machine from the google account and reconnect it. What this looks like in a cryptomator vault is the vault will only has a few of its folders present (compared to looking at the same vault on mobile and all the folders will be visible).
Do vaults contain any checksums or ways to verify if there are folders missing in the decrypted view or if there are any orphaned encrypted files that are failing decryption?