[Zubersoft]

Go to Settings->Other Settings->Find Missing Files and there is an option to delete all of the songs listed. That's going to remove all the annotations though. I recognize this is not what you want - there is nothing that matches what you are asking for. If you rearrange the files that MobileSheets is referencing, it's going to cause chaos. If you don't let MobileSheets manage your files though, that's on you to fix. If it's okay to just delete the songs that no longer correctly reference their file, then that will work.

Mike