If you're forced to swap a Bishop for a Knight but can decide which bishop to give up, is it better to swap the good bishop (In which case your remaining bishop will be bad but so would the opponents unopposed Bishop) or should you swap the bad Bishop (in which case your remaining bishop will be good but so would the opponents unopposed Bishop)

Which is better??

Huh? If you swap your bad bishop, why does that automatically mean that your opponent has a good bishop? You should always swap your bad bishop. In addition, in what scenario would either bishop be able to capture the same knight?!? It would have to be a couple of moves in a combination.

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A "bad" bishop means that your pawns restrict its movement, i.e. the pawns are either all on black squares or all on white squares.  If you develop your pawns as recommended by Nimzowitsch, Seirawan, et. al., you should end up with chains of pawns on like-colored squares.  If your pawns restrict your bishop's movement, then of course they will restrict your opponent's movement as well, and he will have a "bad bishop" as well.

I know, but you're talking about trading bishops with knights. When you say, trading your good bishop for a knight will result in both players having bad bishops, your opponent will ALSO have his good bishop, and you will have the disadvantage!

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No, that's not how it works. If his pawns are lets say clogging up the dark squares center for his dark square bishop, then he has a "bad bishop" ... and yes those same pawns are hindering your dark square Bishop's mobility too, sure, but because those pawns are also targets for your Bishop, your Bishop isn't 'bad.'

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 Please let me clarify

For your second question here is an example diagram (please do not judge the diagram as it may be biased).

 Also the question of Good/Bad bishop relies on blocked pawns (e.g. White's pawns are stuck on light squares and Black's on dark squares) If white has a Knight and his light squared Bishop and black has both bishops white's bishop is bad. However the most likely trade of Bishops leaves White with a Knight and Black with his dark squared Bishop. Since Black's Bishop is bad this endgame favours white.