If possible, I think a flag made by a banned user linked to a missing thread should be auto-deleted, but being invalidated is just as good. They are far more useless than untrusted ratings.
There are several options here.
User can be banned because of old plagiarism. This ban does not mean anything if he creates a flag with real proof and has enough support to be active. It can only be towards inactive flags created by a banned user. Also, I find a few flags where flag creator has not associated thread opener and they haven't control to keep live thread.
Surely if a flag exists for a thread that no longer exists it means the alleged evidence the flag was created on is not available therefore the flag should not exist either.
I wonder what the community consensus is on this.