Depends where the switching happens. If it happens locally to the battery then the cable will appear to connect them in parallel, but one or the other batteries will have turned itself off.
It seems possible (hypothesis, not fact) that something after the cables converge has the intelligence to tell the batteries when to turn on and off. It is that that need reprogramming so that it can give switching advice to the two batteries. If you just connect two batteries with the same cable but do NOT reprogram then the batteries will indeed be connected in parallel.
Actually I suspect that the controller can talk to each battery pack individually, via a serial link, and can turn each pack on and off with the on/off switching being down inside each pack.
The power lines of each pack could then be wired in parallel but I'm not sure whether the serial control lines could be paralleled up.
Either way, the controller firmware would need to be updated if it needed to control 2 packs rather than one.
The point I've being trying to make is that both packs are NOT active at the same time.