Had this come up in a match tonight.

My Lothal Rebel was running FCS and Weapons Engineer. I had target locks on Manaroo and Bossk. Manaroo uses her ability to pass the other red target lock token to Bossk, so both are now on him. Would it now be discarded completely? I'm not acquiring a blue target lock token, and I cannot maintain two locks on the same target.

It would be discarded because you cannot maintain two target locks on the same target, and Weapons Engineer doesn't change that rule.