dr_frost_dk is asking You (andy_con) how You connected both batteries together (we know that in parallel - at least I hope so - but, is it soldered, just tight-contact or whatsnot?).

Also, it would be like if You could perform some current tests with bq27200.sh 5 or, if You prefer that, batterygraph/batteryeye.

It may be totally unrelated to batteries, just something in software, waking up CPU.