This kind of confirms my suspicion that maybe I should have gone with a different idea of mine. (Or, now that I think about it, maybe my idea would have worked better with a different genre, one where the computer normally decides when a battle or whatever is over rather than one allows free movement… (…wonder if I could tweak this game so that that works better… now thinking of ideas for some more major modifications…)).
Exiting and re-entering a room completely resets the enemies in the room. I didn't realize that particular aspect would be confusing.