The only potential thing I was worried about when this happened to me was he split of the partner PNR becoming problematic. A couple of years ago, wife and I were flying a domestic short hop connecting to an NH TPAC, and was quite scared that if a split happened, it would cause a problem for the partner segment. So I specifically told the agent at checkin not to split of. Of course, they did anyway.

Turns out nothing abnormal happened. I called NH right after clearing security to ensure everything was still in order with them, and it turns out it wasn't a problem, though I believe our NH PNR was split as well. Was worried that would be an issue, but boarding, etc. went smoothly.