AFAIK, the reset feature on the AP and disconnecting the neg battery term is the same.
There was at least a couple threads where people's problems ceased when they got rid of running the RT when it was the same as the Base (it was a vf34/30 problem i believe). Just don't do it. If you're running a realtime you want to get rid of, just reset the ECU, don't reload the same base as RT. In theory it should be harmless, but other circumstances have proven otherwise.