Wheels, I think I understand what you're saying.
A normal patch would overwrite an existing file in an existing location, or create a new file in a new location.
So I think you're saying that a patch could easily place the amended mission file in the US folder but the old faulty mission would still exist unchanged in the UN folder as well because they can't delete it.
If that is the case I would get around that by having a prominent note in the Readme file of the patch asking players to delete the old file in the UN folder manually. And if players don't read that note, well, no harm done. Those people just have two versions of the mission ... one which works the way it did before, and the other that is fixed ... and the rest of us have the fixed one in the correct folder!
Same for the other US P-40B mission.