I'm no HVAC expert. The following is based on reason and common (to me) sense:
how would the system react?
I would presume that if you've got line set
A connected to an interior unit to which you've connected the electronic controls for unit
B (and vice-versa), at best you're going to get very limited cooling and in the wrong place. It's quite likely, though, that the outdoor unit will be pumping refrigerant through a line set connected to a currently inactive indoor unit and that indoor unit will end up freezing up because there's no fan running to blow warm air over the fins and exchange heat.
With frozen lines, you'll get very little cooling at all, and possibly damage the indoor unit, the line set and outdoor unit should lines split somewhere.
I would suspect (remember, I'm no HVAC expert, this is applied reasoning), that if you were to turn the system on and crank the AC up in one room, you should be able to hear the outdoor unit kick on, then start to feel cold air move in that room. If things are cross-wired, you might notice a slight cooling, but you won't feel the air moving. If you feel it blowing warmish air from the other indoor unit, you know you've got the wiring crossed. If it's crossed, shut everything off (at the breaker and/or disconnect) swap the wiring at the outdoor unit, and all should be good.