It's unclear what you are trying to do. But here is some general advice:
First, find out where MC thinks the cover art is now.
Shut down MC completely.
Now, go to the cover art location from above and move everything where you want your cover art to be located.
Make sure it's just cover art and not a mixture of art and music files (you indicated above that this had happened at one time.)
So now you should have just cover art, in a place where MC does NOT KNOW where it is.
Start up MC. Change the cover art location to the new directory.
I would expect this change to happen instantly because MC is not moving any files.
Brian.