by no means know for sure, but I think your only options are to replace one with another, or us the new one to traint he old one. BUT it appears the old one losses the original ability and gains the new one. I dont know for sure as my extra BO all have crappy upgrade powers so I dont want to swap um yet.
You could try to sell them off, I think it should work if they were never assigned to specific Bridge Stations on your ship, but I may be wrong here.
You could play around with their skill-set, or buy/train different skills for them and make an alternate Bridge Crew setup. I have for example two Science Officers, both are Lieutenants now but with my current ship, one has to use the Ensign Science Station while the other can use the Lieutenant Science Station, this means that out of combat I can switch between the Officers and have different skills to use in combat.
You could set up a bridge team and an away team. Or you could have alternate options for both. Like you want tractor beam for one encoutner but want Jam Sensors for another and only have one science slot on your ship. There are lots of reasons to ahve extra BO's.