Well, from the symptoms you describe the problem is somewhere between the batteries and the converter. I could speculate a bit but maybe it is better to download Thor's General Schematics file for your coach. It gives electrical, plumbing and other isometric schematics of your specific coach.
You can find it by registering at https://www.thormotorcoach.com/owner-resource/
with your VIN. Then look at the documents available and find the schematics file and then look for the DC schematic.
Mine shows a 50A breaker to the battery then to a heavy switch and then the wire goes to the converter DC in terminal. Instead of a simple on/off switch like mine, yours may have a relay that is actuated by the use/store switch that may be bad. My suspicion is that this relay is in the box you found. There should be heavy DC in and out wires to/from the relay and two light gauge wires from the use/store switch exactly like you describe.