Well that's the thing isn't it? Before Isolation, there was no Sevastopol, no Torrens. Who knows how many other places that have yet to be created and brought into canon, that could more easily explain where the eggs came from?
On a side note, I'm having a very hard time believing that a company with such resources and a colony on LV-426 could have such a difficult time and constantly fail to gather specimens. Surely before or during the time the colony was being built, or during the early days of the colony, the company could've gotten their hands on something? Of course that would mean Burke was really out of the loop, but we didn't get to see the egg chamber. So who knows how many may have been missing by the time Newts parents got there?
I think they got what they needed, and have a company owned and operated Hive somewhere.