Also, we've done test and it seems if you save your game by using the In-Game
Save option, the newly edited flags aren't responding or colliding with other
flags that we've either changed or deleted. So for future reference everyone,
when you save your game, please go to your emulator and select File-Save
Game-and save it into any Slot. You can use that save file anytime for any of
the patches & it SHOULD keep your saved data with all of the updates the
patches bring every time. Thank You.
The game will screw up the flags either way, the game saves after you beat the Pokemon League so it will naturally screw up the flags, if you get what I'm saying.