Do you fancy the theory that maybe the engineers/space jockeys believed the xenomorphs were extinct, maybe just a legend, or myth from their past?
I say this only to spark some ideas but here are my reasonings (feel free to add):
The Space Jockey I, in my personal opinion, think the Space Jockey and Engineers were two separate branches of the same species. Anyhow, in Alien, the Jockey appears fossilized and the ship seems as though it has been there for thousands of years, abandoned. God knows how long that distress beacon was going on for, but clearly no one wanted to find them, or maybe they were just that cut off from everyone else. The eggs below/within the ship seemed as though they hadn't been disturbed since the fate of the Jockey, so I assume they are just as old, and have been there for just as long as old elephant head has been decaying.
The Mural in Prometheus we all know of the xenomorph-looking depiction on the wall. Considering that engineers pre-date humans this means the mural could be thousands of years old. Maybe something they worshipped? Or feared (As if it were a sculpture of their Devil)? Or simply were fascinated by it?
David finally, the Android David stumbles upon some blueprints, thus allowing him to recreate the xenomorph. This just made me think that xenomorph must be an older species that the Engineers/Jockeys knew about. Also, when David attacks those Engineers with the black goo they seem so confused as to what it is, as if they're encountering it for the first time. I know it's not the xenomorph but it seems to go with the idea that the engineers had lost a part of their history.
Conclusion:
So, where am I getting at?
The Engineers/Space Jockeys are thousands maybe millions of years old. What if the xenomorphs were from an earlier time period of their species. Maybe they were used for war? Whatever their purpose, though, the xenomorph was eventually lost or forgotten, maybe put away from certain tyrants who would abuse it's power, or they just tried to remove it from history as best they could. Eventually, it became myth or legend to the younger and younger generations of the Engineers/Jockeys as they drifted further from their past. So, the xenomorph became extinct in the sense of losing part of their culture, or so they thought. Eventually, it would become unearthed and unleashed. Whether it was the events of David, or Alien, or something we haven't seen on screen, the xenomorph -an ancient mythological species- was brought back to light...
Similarly to how on Earth we have Pyramids and certain remanats of the past that no one has an explanation for, only theories.
When I picture this in my head I think of something similar to Lord of the Rings. How there were different ages and eventually all of the talk of the One Ring, which at one point was a very serious thing to everyone, died out and was lost, becoming myth. The only thing connecting their present with that past was stories or statues, slowly making it less 'real'. Then one day, it resurfaced, of course, causing chaos.
Thanks for reading!