I am sure if there was a short circuit, a fusible link would have worked. I think the APU battery is only used for a couple of things, so a short circuit would have been easy to identify as the problem. There would have been lots of heat damage in a small area. I think anything easy to identifyas the problem, would have already been identified.
I think they will only find it while the entire system is operating, probably in flight. The question is how to do that with a degree of safety that is acceptable.
I don't think disconnecting the battery in flight is enough. Lithium cells can be damaged, but not go nuclear for quite a while later.