Also suffering from this issue. Posted in Blue's thread https://project8.dev/threads/file-verification-failure-unknown-file-not-found-in-manifest.11739/
I am suffering from the exact same problem. Missing files seem to be the exact same.
Main difference is that my Steam Cloud is up-to-date to seems to be unrelated.
I have attempted to Verify integrity of game files, Reinstall, and manually delete the entire Project 8 folder in steamapps...