unanswered PPRE Help: How to set flags in script editing [Gen IV/4]

[ZephyrosDS]

So I'm coming along with my Spirit Silver hack pretty nicely and I have implemented a lot of new content, as well as, many new trainer battles. One such being able to fight a Battle Frontier Brain early on. He blocks the gym from being used and you must battle him before entering as a test (per se). Now I have scripted this whole scenario. He will walk away from the gym and not block your path however when you exit the map and go back in he reappears. Now I know this issue can be solved by using Flags but I am not quite sure how to utilize Flags in this instance. PPRE gets rid of my flag when I add it onto the script. (I would go to another map on PPRE to edit, then come back and it will have been removed). So my question is, How do you use Flags in PPRE correctly for Pokemon Soul Silver?

This is my script.

Lockall

Faceplayer

Message 28

WaitButton

CloseMsgOnKeyPress

TrainerBattle 80 0 1

CheckTrainerLost 0x800c

If 0x800c 0

Message 29

WaitButton

CloseMsgOnKeyPress

Applymovement 13 mov_7

Waitmovement

Removepeople 13

Releaseall

End