That's not completely correct. During the 1999 Kargil War either Pakistan invaded India or vice versa (depending on where you believe the legitimate border lies). Both countries had atomic weapons as of 1998.
https://en.wikipedia.org/wiki/Kargil_War
I had not considered that conflict. It was in Kashmir and the border was never agreed upon by both sides (as you state). I wouldn't call it an invasion or even really a "war" with the small number of killed at only ~1,000. Others might disagree.