I'm not entirely sure I understand your question, but I'll give it a shot anyway...
Okay, this is my basic understanding (please correct me if I'm wrong
). You want to fight an NPC blocking your path, and when you win, he disappears with a magical flourish of wonder and majesty. But when you come back, he's back too, and you have to fight him again.
There's a very easy fix for this: you could either assign that monster to a switch which toggles back on when you leave the map, or you could use the wonderfully obscure Erase Event command (although you should almost never use that command; make sure you clearly understand how switches work if you want to take this shortcut). So say you run into the NPC (maybe with a set by collision event where he says "You... Shall not... Pass!" like Gandalf), then initiate the battle. The very next line should just say Erase Event, and *poof*, no more monster. The good thing about Erase Event, though, is that the event reappears when you leave & come back.
Again, correct me if I misunderstood your question...