As i think about this more, this is still puzzle. The anderson connectors disconnect the second battery positive and negative. that said, the topper light wire is connected directly to the positive on the second battery...which goes back to having to track the grounding of those lights.
Nope, as Hotrod indicates below, you are removing the ground for the battery when you disconnect the Andersen. Think of it this way. You have to have a complete loop from the battery positive back to the battery negative to create a circuit. The most basic circuit would be: (a) Battery + terminal, (b) a wire going from battery + terminal to lightbulb wire in, (c) lightbulb filiment, which lights up, (d) wire going from lightbulp wire out to out to Battery - terminal. You have a complete loop from Battery + to Battery -.
What you have: (a) Auxiliary Battery + terminal, (b) wire from Auxiliary Battery + terminal to lightbulb wire in, (c) lightbulb filiment, (d) wire going from lightbulb wire out to truck frame, (e) wire going from to truck frame to Primary Battery - terminal, (f) wire going from Primary Battery - terminal to Andersen Connector, (g) wire going from Andresen connector to Auxiliary Battery - terminal. That's your complete loop.
When you disconnect the Andersen connector you are breaking the circuit loop at the (f) to (g) stage. The fact that you have ground to the primary battery is irrelevant.
If you run a ground from the Auxiliary Battery - terminal to the truck then steps (e) through (g) above are covered by the wire going from truck frame to Auxiliary Battery - terminal. Then the Andersen connector doesn't play a role in whether the lights connected to the Aux battery go on.