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For anyone who might be looking for this in the future, this was the issue I had. Simply leaving and re-entering the zone made it work as expected. Wish I figured that out sooner!
Thank you for the help, and for dropping that rather interesting fact. I'm still trying to learn a lot about gen 3...
I have a script that starts a fight, fades the screen and sets a flag. I have the flag set within the sprites person id within advance map.
The problem is the person even will disappear after the fight from the hidesprite function, but reappears whenever you take a step. HOWEVER, if you leave...