The message clearly states the the files listed are not where MB expects them to be. This could due to you deleting from using an application other than MB. Such as a file explorer. You should never move or delete files outside of MB as MB will no longer know where they are. As the message states.
Do you know if the files exist -any-where? If you know where they are you can either move them back to where they were using the File Organizer. Or you can File > Add Files to Library.