So I have the three pieces of the Breen Absolute Zero Set, but the set bonus is not being applied. When I look at the deflector after equipping the set it says 1/3 but when I look at the shields and impulse engines it says 2/3 for both of them....

Are all those items the same mk level ?

Oh I see... the deflector is Mk II but the others are Mk IV.... well it's not my fault that I was promoted halfway through the mission arc.

Well, it actually is.

But don´t worry , one more Breen mission in addition to do three of them again each time you rank up is not that bad.

Wait what? I can repeat them??? I did not know that!!

Go to your ship's bridge, and find your ready room.

Your desk has a computer terminal on it through which you can access any main story or episode mission that you have already completed, for the option to replay it (with all associated rewards)

yes you sure can and they really need to explain that in game.

unless people come to the forums a lot or happen to stumble across your ready room, then chances are you wont know it.