Wiring for dual batteries question

[TallRedRider]

I have an 06 X45 with dual batteries and a voltage sensitive relay. I was closely looking at how they are wired up and have a question.

I have the amps and stereo all getting power straight from battery 2.

The starter comes from the perko switch. There is a wire that comes from the perko switch that goes to a 90 amp main fuse and then into the guts of the boat.

There is another set of wires that come directly from the black box on the port side storage where the ballast fuses are and goes straight to battery 1, bypassing the VSR and Perko switch. There is both a ground and a power wire that come from there.

So the question is: what are those wires doing directly wired to the battery? Following is a picture with battery number 1 removed.

I see this as a potential problem to leave both batteries dead because they bypass the perko and isolator. I can run down battery 2 with the stereo and then I can run down battery 1 with the ballast pumps and whatever else comes off of there. Could this leave me with 2 dead batteries?

Thanks for any thoughts or opinions you might have.