If that board gets scrambled, a reset will usually fix anything like a board that gets locked in a direction. I would not run a board set with a known dead battery. That's even if the battery was brand new. They need to be charged. A low battery isn't like a dead battery.
Whatever you decide, charge it first. Even the BCR2 needs charging although it's only for a minute or two. The do have a lifespan though that seems to be equal to the blue batteries. I tend to go with the stock batteries and others prefer the BCR2. I have had around 100 MTH board sets. I had an instance where the board set did not like the BCR2 so I installed a new battery. I did not know why this happened. Another poster/ MTH tech who I respect, suggested sticking with the batteries.
I did not know that the caps in the BCR's have a limited life span and they don't like heat either. Although they can charge faster, I have a ton of engines that still perform perfectly with their stock batteries for well over a decade. Just running them a few times a year, at the least.