The Khmer Rouge were quite happy to kill any Vietnamese they came across: civilian, or Military from North or South. They were fairly racist on that. The KR had started purges in 1974, continuing what Lon Nol had started with his anti-Vietnamese pogroms. It was one of the few things that Lon Nol and Pol Pot shared belief in.
I don't think Pol Pot is insane enough to consider North and South Vietnam indistinguishable, or to not be able to pick a preferred enemy.