I’ve found adding the files, with the exact same naming, back to the folder with the redirectors that won’t clean up seems to either resolve or overwrite their redirector; I then move the files again and it seems to clean up properly (or I re-do that approach until it does).
I am not sure what would happen if I was to do this with a dummy file of the same name but I did not want to risk breaking it so I did not try that.
Unfortunately I had renamed a bunch of files so I had to rename them back, and then rename them again after the redirectors were cleaned up properly.