Did Pep Boys replace it with one that had the exact same specs as the original? If so, then yes, a BT cable will let you reset the battery adaptation. Otherwise, you'll need to have the car coded with the specs of the new battery.
2010 535i M Sport - Platinum Gray/Dakota Black/Anthracite Bamboo
JB4 G5 ISO, BMS DCIs, ER Charge Pipe with Forge DVs, Proform Clear Bra, LUX H8 160 LED angel eyes