@lillibolero You tried the "Import from Cloud Storage" function in Media Cloud? I think that's a pro only feature, but it will attempt to sync up storage with your media library. Media Cloud tries to make a best guess when importing from cloud storage to prevent duplicates, but there isn't enough information in WordPress to make that entirely foolproof. Depending on how big your media library is, I'd setup a test dev site and run the import from cloud storage batch tool and see what the results are.