I think there's a better way to address the problem... Each item on your panel has an associated double pole, center off power switch. So every item can be individually connected to one battery or the other. When you are powering up your panel, you assigned batteries to the various gadgets in a way that pretty much balances the load.

This approach means that there isn't any switching batteries in flight. You never need to think about it. It also means that you don't have to deal with the question of how low should I draw battery 1 down before switching to battery 2. For all battery types it's better to not be drawing them down deeply if you want to maximize their life; splitting the load evenly is thus better for overall battery life. And, of course, you preclude this problem of switching transient.