Time isn't a factor. If the specimens were destroyed, they're not going to 'get better'.
So... maybe they weren't destroyed at all.
Maybe the company guys in Alien Resurrection are simply incorrect, misinformed or have been deliberately misled.
I think Alien 3 can be somewhat waved away with the urgency of getting and containing the Queen ASAP. But yeah, the ballache that the USM go through to clone Ripley wouldn't have been necessary if they could have just visited LV-426 again.
So that either means that the AP explosion in Aliens meant the Derelict wasn't a source of eggs anymore (radiation sterilising the eggs, the Derelict was actually destroyed) or there's some unknown incident that took place in-between Alien 3 and Resurrection that also meant the Derelict is no longer a source of the eggs. I think there's plenty of room for the second option.