I just replaced my dying factory FLA batteries with 2 X 100Ah LiFePO4 units. To do this, I had to disconnect the batteries while the controller was up and running and it was a sunny day. I actually considered pulling the 3 rooftop panel connectors out of the 3 way combiner, but after consulting Winnebago Tech Support, they said no need.
My system is a factory installed Zamp Solar setup, 3 X 100W panels and the ZS-30A PWM controller. When all was reconnected, everything is up and running with no apparent ill effects. So, I'm going to *assume* this charge controller doesn't care if you disconnect the batteries, either at the battery terminals manually, or with an added disconnect switch. Which I didn't add. Never ocurred to me to add one.
Just in case you've got the same, or similar, setup.
