Well, the obvious point is his hair isn't the white it use to be pre-Flashpoint.
But after reading Batgirl No. 5, it seems like more has happened than just a bit of de-aging.
* Are we back to the pre-CoIE status of Jim Gordon being the natural birth father of Barbara?
* Has his marriage to Sarah Essen been completely erased from his history?
In Batgirl 5, Babs is visited by a woman with red hair who's supposedly her mother, and we learn that she's been out of Barbara's and Jim's life for some time. Plus, while the two are having muffins and coffee, Barbara thinks "The kid in me wants to defend Dad - - doesn't want her to know how hurt he was, how he never remarried."
* Does Jim Gordon not know that Babara is Batgirl in the DCnU version?
Also in Batgirl 5, Jim is trying to get Detecive McKenna back to work, with a case that involves Batgirl, and tells McKenna "I want her found, Detective. You're the best I've got. I want you on this. Are you able to do that objectively, given your history?"
So, does this mean the DCnU Jim Gordon is clueless as to Babs' double-identity?
One has to wonder how likely the DCnU Jim Gordon is to know about whether Batman is Bruce Wayne or not now. Also, I don't think Jim's son James Jr. and his recent past activities have been brought up in the DCnU yet, aside from a possible cameo appearance in Batman 1.
(But then again, wasn't it Detective Comics 1 and Batman 1 where we had the confusion over whether Jeremiah Arkham had ever been Black Mask in the DCnU, or was he back to being the head of Arkham Asylun again?)