Has anyone had experience with installing a re manufactured, reprogrammed ECM and then immediately started getting new "check engine" codes that were not there before?

I got the unit pre-programmed from Napa to solve my "battery not charging issue", and the charging issue is resolved but now the codes appear but according to Napa it is not the problem. I don't really want to fight it.

Anyway, just curious if this is a common thing or not. The codes were not there before the change. The charging issue is fixed, btw.

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