Every time I did that they re-appeared... Quicker! I tried multiple times to re-set the instance, only to have them pop right back in. Then I tried to scoop and run, just got even more banged up because I needed 4 and only had time to scoop 1. Then I decided to fight back, killed them all, had my hull down to 23% and couldn't find the mission cargo. Re-set the instance and they're baaaa-aaa--aaacccckkk!!!
Got so mad I flew back, parked the Asp Scout, jumped in my FAS... Killed them all (now for the second time in this mission), kept the fight near the cargoso I scooped and went home. In my experience, they will always reappear. So from now on, I do these missions with my FAS... Wait 30 seconds or so before I go for the cargo with weapons deployed. The instant they pop in, target the highest ranked, kill him with extreme prejudice... Target the next highest, usually the lowest ranks will run after you cap the big'uns.
Your mileage may vary...