Alright so I was curious. Could you trade away a feat for another feat if it was a bonus feat that you got from multiple sources? For example a Monk who goes Sacred Fist gains Improved Unarmed Strike twice, well that second time it rather pointless. Would you allow for them to retrain that feat even though its a bonus feat? Or could you even given RAW or RAI?
No; you cannot retrain bonus feats into something completely different.
If someone took Improved Unarmed Strike as a regular feat and then gained it later as a bonus feat, then retraining his regular feat selection is fine. If you chose the feat from a list of bonus feats (like the Ranger's combat styles or the Fighter's combat feats) then retraining to another one on the same list is also fine. If the class feature gives you a specific feat, then you're stuck with that feat. If two classes give the same feat, then you're stuck with a duplicate.