Sadly, the battery is likely ruined. If the computer is telling you to do this, then it has already detected the battery in a weakened state and alerting you to imminent failure (battery probably can't be charged to full capacity any longer).
However, I'm surprised the battery became completely discharged. The systems are configured to shutdown everything (including courtesy lights when the doors are left open) after about 15 minutes of no activity. Only things that are hotwired (blinkers, parking lights, ignition, etc.) would remain on at all times. Maybe something else was left on?
Regardless, lead acid batteries never like to be completely discharged--it's a death sentence. I would follow the computers recommendation as I believe it's an accurate assessment. It's not something you can reset as far as I know.
2013 X3 28i (prem, tech, cold1&2, conv, hud)