At some point the authorities in the two counties, most likely the respective District Attorney offices, got together (perhaps over the phone) and made the decision that County B would go forward with its case and County A would not. I do not see where he would need to have been consulted or that the local authorities were required to specificly consult with him on that decision. This may or may not have happened after a court appearance or two before that decision was made and perhaps he did have to appear in court to learn that County A was dismissing its case. For all we know, maybe he thought that if County A was dropping charges, County B would soon do likewise. If he had legal representation in County A, I suspect that his or her attorney or public defender did the job expected.
County A, however, originally had filed charges, so it had to notify its court that it was dismissing its charges. County B then proceeded with its case, which ultimately ended in him accepting a plea bargain. I do not see any double jeapordy here. If anything, the counties in question recognized that this issue possibly existed and took steps to resolve it.
I do know that in retrospect that it looks like if County A had prosecuted and County B had not, he might have only been convicted of a misdemeanor and probably had fewer difficulites with employment, today. But, your son was not the legal position to choose which county was to pursue its case. It also was not something that his attorney likely could have controlled or influenced either.