If the two batteries are connected by a positive to positive wire and then a neg to frame and a neg to frame, so that the frame is part of the neg path paralleling the batts, AND then, you have the rig's "load" wires on the pos and neg of one of the batteries (leaving the other batt as the "downstream battery" )--- then, if you put a disconnect switch on the neg post of the battery with the load wires on it, that will leave the other battery running the rig's 12v.
It has the positive path connected, and it has its own neg path to the frame. The rig's neg side of its DC panel is connected to the frame making the neg path complete.
You can fix that and use a neg side disconnect switch if you run a wire neg to neg battery, not using the frame, so that one only one battery is connected to the frame AND you arrange the rig's load wires so that the neg load wire(s) go to that same neg post AND put your neg side disconnect switch there.