I recently picked up the Dhelan Retrofit and slotted the Aegis deflector, and the science bridge officer abilities and sabotage probe are greyed out, as if it's just not equipped. I get all of the other bonuses from it, the shield power, the skill boosts and the set bonus, but I just don't get to use any science bridge officer abilities. Slotting a basic deflector works fine, however.
Edit: Oh, and the Fleet Dhelan also doesn't seem to like the Aegis deflector.
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