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Given your description of the problem, it sounds like something electronic was going intermittent. That is probably the worst type of problem to diagnose, total failure is much easier. Nikon may have figured it was better to replace the electronics in total than to do it pieces at a time and have you send it back repeatedly. It's also possible that whatever failed fried or shorted other things. The flexible printed circuit "board" (or any PCB for that matter) has many components that can fail. The usual course is to replace the entire board and if cost effective, have the board re-conditioned by a specialty shop. It's rare that these are cost effective to rebuild, most companies send the take outs for recycling.
In your case, bad contacts in the lens mount could push voltage into parts of the lens that shouldn't have voltage and thus the damage.