I tried the omni cheat. No dice. It's not so much that I'm losing contact as they are moving past me and I can't attack them. And no, I don't have a treaty with them. Random events are set to low occurrence and severity.
The reason why you can't attack is because there ships are unknown, but I can't come up with any ideas why they would be unknown if you have direct sight of them. It might be worthwhile to forward the savegame to MM, just let him know which version of the mod you are using and if you were using any custom shipsets etc. It has to be some sort of bug.