I got to experience this firsthand because it happened to me. I learned a command, decided I didn't want it on that button so tried to delete it, and everything described above happened to me also.

I finally gave up and left the command on the button it was originally learned on, but of course now I can't clear that screen or do anything with it, unless I do a complete reset, which I am not going to do. Luckily it is a utility screen with some rarely used commands for my TV so it is not much of a bother to me.

I always answer these questions for problems which never happened to me, but now it has so of course I understand all of your frustrations.