Since the ships are spawned on patrol paths and not via pop zones, their spawning/despawning behavior is a bit different. We either change the spawn to zones instead of paths or add that to the list of things the code gang needs to look into.
Btw I forgot about this, but I think I have more info now. During farming, the "mothership" of the pod has to be within ~6K, or the whole pod de-spawns. So for Hel + 2GB it's the Hel, and they sometimes tend to cruise towards the jumpgate to shoot at it, while the gunboats engage you.
I think previously they could literally despawn right in front of you, but now if you are near the mothership you should be good. At least I haven't had issues over multiple hours of doing this.