So now I am charging the battery on a trickle charger to get it back up to normal range. I will then see if the ACR switches off of the "under voltage isolation" mode.
Yes, but!! Only as long as it holds a charge (the battery is still "ok") and the battery's "resting" voltage is remaining above the "under voltage lock out threshold" of the ACR. Not sure what that is, depends on the manu and Blue Sea has changed it a few times now, think its around 10.5 to 11V, not sure, you'll have to look it up.
Question: When the ACR is in the isolation mode, does it still send a charge to the battery?
No, not to the house battery. Yes, to the motor battery.....
I am wondering if, hypothetically, I left the battery switch on over night and the fuse box drew down the battery to a point where the ACR "isolated" it.
Yes, you most likely left something on in the house circuit side and have dis-charged the house batt down so far that the ACR locked it out of the charge circuit............This is the fickle part of an ACR/VSR and based on my needs, I don't particularly care for as it can't isolate(like exactly and simply what you're having to do right now with the trickle charger) and charge JUST its aux/house batteries, it can only parallel them to charge.......arrrrg!!.
Hence, it knows better/is designed then not to parallel your/a very/ish discharged battery with your/a good motor battery..........Current inrush at parallel time/wiring would go off the charts.
You mechanics out there must be enjoying this....
Not a mech but, I do have a few wrenches .......At least you're asking and trying to learn, its all good man, np.