His initial reasoning was because the alternator is a connection point to the BDS line. It turned out he didn't have to change it after running diagnostics (to both our relief...he says my car is the best maintained out of the cars he works on).
The codes were wonky- they didn't match the warning indicators on my dash. The water pump and thermostat were working just fine. The mechanic reprogrammed the car. Day two of driving and it's not giving me any issues. Cross your fingers it was just in need of a re-sync.
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