I doubt there is any damage to the Cbox.. If those ports still work, then they worked as designed..
Yes solder 2 outputs as you described.. You will then get all the isolation and telemetry..
Now.. that said, recommend you get a set of A123's and wire them in direct, and use the CBOX mag switch as it is designed to do.. It gives full battery redundancy.. The Gemini of course is a good system, but its only a 6 amp peak per channel.. could be a little light depending on the size of the airplane..
If you wire batteries direct into the Cbox as it is intended, it will handle 50 amps no problem total load..