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so I'm @ that dungeon where you have to play the flute to those dragon doors, bad enough that I had to use a FAQ since they don't really explain it in the game but I can't get so many of the doors open especially the ones that change colors, so after wasting a few hours getting the tune wrong and facing countless battles I've decided enough was enough, so congrats to Star Ocean 3, I have never gotten so frustrated with a game in such a long time, not gonna waste anymore time on this
I never really was bothered by the MP death thing. Very few bosses actually do enough MP damage to kill you before they would HP kill you anyway and those that do tend to die very quickly anyway.
I'm pretty sure you don't need to go through the doors that change to get through that dungeon, you only get some extra (and nice) items, although I might be wrong.
Make sure you've raised the Attack and Defence stats as that can make the AI die slightly less often, although they still aren't good enough to rely on. Alternatively, you could unequip the MP draining moves so they only drain their HP, or use the "Don't use coup de gras" tactic so the AI doesn't use battle skills.