They may have just figured it a lost cause, there could be radiation, maybe if it had been buried by geologic activity it was not accessible.
Maybe after the disaster at Fury 161 and Hadley's hope, WY scrapped the whole Alien project, and very possibly a fiscal decision was made to cut their losses.
They may have also checked out LV-426 found that the derelict had been so deeply buried, and was surrounded by so much radiation that this only helped make the decision to cut losses.
I mean if WY wanted the Alien so bad, they could have cloned Ripley right after what happened on Fury 161 then too. If they have inter Galactic space ships, and androids, then I think they could already clone a human. It did not take 200 years of R&D to get it right. I think no one attempted it until far later.
For some reason her blood sat on ice for 200 years, and that may be the same reason no one messed with the derelict, WY cutting their losses.
When the USM took over the records, they decided to investigate all options, and to re-open the Alien file.
They may have set up multiple teams, all working around the clock, not putting all eggs in the same basket. At the same time one is cloning Ripley, another could be back on LV-426, with a massive dig crew, going deep underground to uncover the lost Derelict.
None of these options are going to be "perfect" back stories, but they are far easier on continuity than say AVP and AVPR. It not like there were not other illogical ideas in other Alien films. The point is it could pass for logical enough to use as a source of Aliens in an A5.
Then there is Aliens coming from the Derelict before Hadleys hope was built.
The source of Aliens in an A5 could come from a lost human ship that may have encountered the Derelict in that 57 year gap from A1 to A2.
Say a decent sized human ship gets an alien onboard, which leads to a Queen and a whole hive, not unlike Hadleys hope, and the ship ends up adrift in space, lost for 300 years. Maybe all the Aliens in it have died off, or are just Hibernating, but at least plenty of eggs remain. The ship gets found etc...