If it is wrecked and BMW didn't do the repair they may tell you not their problem and be willing to fix it but at your cost.
Now on to your problem. I agree it isn't clear to me what you are saying. If I understood you, you disconnected the battery at one point with the car running? Big no-no for this car by the way since it has an Intelligent Battery Sensor (IBS).
Specifically what does your Idrive message say?
There is a chance that your IBS is toast or that as you mentioned the cable harness to the back of the fuse box is at issue. If the cable connector is the problem you may have to pound on the glove box to start the car. If that helps the car start then that is your issue and BMW should do the recall if your year is effected.
The BMW charging system in this car is not a simple alternator-voltage regulator-battery affair. The DME using inputs from many sources like the IBS determines how much charge the battery gets.
Measuring the voltage to the battery would help determine if your alternator is healthy too.
Not sure I touched on the issue...