Any way to validate that all files and folders are present in vault?

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?

You can perform a vault health check. It will detect (local) orphaned files/folders.
But this does not check your online vault. And cryptomator desktop also does not connect to your online storage, so no way the desktop app could detect missing online files. If the sync client does not perform the sync correctly, it’s up to the sync client to report that something is wrong.

Yes, I see the health check option now and will give it a try next time I encounter this issue. Thanks!

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