You guys would be doing this without his consent, yes? Because he prefers what he is now and didn't even want to change back for his best friend/lover.
Whose consent? In the game we are talking to Mindflayer with memories of the Baldurian. Of course he has no investment in getting Baldurian resurrected. It doesn't mean that Baldurian himself wouldn't be happy to be brought back to life.
Does anything prevent the Emperor from continuing to exist if you brought back Balduran with a wish/true res spell? I mena, you could resurrect Balduran (his body is consumed) and they could both exist provided no one tried to go after the other one.
In D&D no.
In whatever Larian fabricated, no idea. There is no internal logic to what Larian does.
The only thing that might prevent a true ressurection is the 200 year time limit. The entire timeline about the emperor is messed up, so no idea when Balduran died.