Ok So my ship that I fly was awarded a new ship from a mission. I temporarily made the reward ship my new flagship, but quickly switched back to my old ship. So now the problem seems to be half of my weapons and special maneuvers are now split between the two ships. I'm talking about those row of ten boxes/slots on your ships tactical view. I currently have the three tiered row of ten boxes. I did nothing to split the weapons, fleet assistance, etc... How do I get those on the reward ship back to where they previously belonged on my original flagship? I hope this wasn't confusing.
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With a new ship you need to set those up again. On PC just click on the top-right of the top bar to bring up your list of powers.
Before that, make sure you have set the Stations for the ship -- which bridge officer is in each of the available seats. Also for those bridge officers learn any new powers you want with training manuals, and switch any powers that no longer make sense. For example if you were using cannons but now use beams, change Cannon Scatter Volley to Beam Fire At Will.
Thanks syrilian!! That did the trick.