I had the exact same problems flashing my car, with it dropping at 2%, then 99%, and it finally went through the 3rd time. I had to turn off the car completely, take my fob and AP out, and sit for about 30 seconds for the car to be completely off. It would then work after all this. Scared the crap out of me, and I'm kind of afraid to switch maps right now. Talking to Rob@Cobb he said it could be my battery (07 on original battery). I've never had any problems with my battery before and it works perfect so I'll prob go and get it tested and see how it's holding up.
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e92, e90, f30 #DieselLife, e46, f80
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