To once again regurgitate the words of my father having posed this to him to see what he'd say (former Chrysler Mechanic Superintendent / experimental test driver)
"My **** broke while in your possession? Not my problem. Functioning when it arrived for free work? Functioning when it leaves, for free."
The rest of the spiel was more of the same - 'if someone breaks your property, they're legally responsible for repairing it, if the BCM fault stops the car from functioning entirely, and you drove it there... meaning it was functioning, they broke it.'
While not uncommon for them to ask for you to split 50/50 on the cost of parts (the idea being, you're getting a new unit so it's life span is renewed), if they want labour or anything beyond that, you have legal grounds to go after them, and they should be made aware that you know that.