So 1 More Question, in Fire Emblem Fates, and Three Houses the other playable characters from other pathways fight each other, if you picked Hoshido, you fight the characters you get in Nohr, and vice versa and Three Houses’ 4 Paths are self-explanatory, but in a GBA Rom Hack is it possible to have 2 Protagonists fight each other without getting a Game Over? It was done in The Last Promise.
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Seems like you answered your own question.
Unless someone has developed ASM to store unit data when a Player Unit is no longer an ally, you would have to make enemy versions of those characters. If you load a player unit as a red or green unit, their data will be deleted from the save file the next time the game is saved, unless they are made an ally again before the save happens.
Killing player units as red or green units will delete their data and trying to load them again will have them at their base stats.
I had a unit who leaves and has to be rerecruited as an enemy, and I had to load him after battle prep to avoid having the player delete his data by saving from the prep screen.
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Boost TLP in the FEBuilder and analyse how it’s scripted, then.