Toeks

My 2005 530d was in for repairs recently and at some stage we were informed the car had an electrical fault (the repairs were all cosmetic due to hail damage). Went to inspect and found the car was totally dead, nothing happened when you turned the key. The had BMW repair it and said the computer only needed to be "Reset", upon which the car came back to life. Now the key they had is not working. It starts the ignition fine, but the buttons don't do squat. The spare key though works fine. They advised that the broken key also needs to be reset.
After enquiring about the fault their technician said these things just happen and that the key and the cars computer problems are unrelated, but I'm not convinced. Can somebody elaborate on how the two fit together and weather my fears are justified that the key is stuffed cause it was in the ignition when they did something wrong which shorted out the cars electronics?
Thanks.
Toeks.