[Solved ... sort of] Resolve Missing Files Problem

Through all of this are you actually missing any audio files, or is cubase just citing as you say?

The pool might be the key. Open pool and right click in it, select remove unused media, not to trash though.

Save , and reopen and if you get missing file message again, choose locate and then set the new path.

The original path you deleted was probably still showing in the pool as the current path therefore cubase was trying to phone home but with the wrong path. With Cubase if you have audio video files and then change the path to them by deleting folders it won’t be able to see them anymore.