While there was the issue with the tool left behind, the general problem with the panels was the close prox that allowed arcing across parallel panels. That was a major redesign early on.
In regards to the batteries, in the fwd EE bay, it appears this is run like a UPS, where the power is constantly being drawn through the battery system, to provide a clean source for the avionics, else there would not have been an issue in-flight.
IF that is the case, the batteries are in constant use.