Hi, sorry for hijacking, but I have a similar problem.
Found this forum searching for the same thing. Disabling the in floor pop ups. The pool I have is over 30 years old and the last time they did a remodel they changed to magnaflow pop ups that I guess even if the system was working correct, they are not big enough to do the job. There are only 7 of them spaced 12 or more feet apart and none of the steps. But that was IF it was working correctly. Its now. The gear mechinism is either broke or was pemanently disabled. 3 of the pop ups, one at the shallow end and 2 at the deep end (24000 gallon diving pool) all pop up every time and never rotate.
I got quotes to fix what I have and every company had the same comment that the current system is fubar.
So I am going to a pool shark pool cleaner. There are no returns other than the pop ups, but I have been told that the system will walk right over the 3 that are work. I was hoping I could pop em out, remove the guts and maybe even drill a hole or series of holes in the top of them for flow. If I can do that, I don't see why I wouldnt be able to lock them in the down position as long as water can flow thru. I don't want to just pop them out and have large holes that can collect debri. But it sounds as if I will have the same problem as the original poster of not having pop ups that are easily "fixed".
Sorry for the long post. This is my first pool.