They came back with two fleets. One popped up, the second one, then the first one, and so they switched. I destroyed ships of both one by one, about a dozen total. Same method - since the same ships are popping up each time, target one and keep the lock on. This time they did it until there were no ships left.
It’s even more bizarre as it turns out that there is another JP in the system, also controlled by that NPR, and yet they never try that thing there.