Check your Inventory screen and see if there's an option for "Overflow Bag." I logged into my current Engineer Fed, and the other forward array and aft array that had been on my Advanced Heavy Cruiser were in there. Can't put them back on my ship, though.
The patch that made them unique probably didnīt account for items already equipped.
While they have been unique for a while, those who had the TOS Connie were able to repeatedly commission and decommission the ship to get extras, and so while you couldn't get any more arrays from the mission rewards, you could own multiple. The unique flagged only stopped you from getting extra through the mission, but didn't stop you from equipping multiples if you had it.
Mission is a succes weapons are returning to their original timeline.
About damn time, when are you going to remove the constitution? damn things outdated and causeing more havok then it solves, figures why we originaly only build 12.