Week Three: The History of Earth

According to the first P.R.O.B.E. anthology, the Durrington Walls (the larger complex of which Stonehenge is a part) is the location of an ancient portal to the Yssgaroth dimension.
The greater site at Durrington (which included larger wooden henges and fortifications around the central area) is 5000 years old. But the stones which WE consider Stonehenge were only errected 2,500 years ago. (This the real-world timeline.)

Geoffrey of Monmouth's timeline starts ~1,200 BC with the arrival of Vicki Pallister's cousin-in-law Aeneas, introducing Trojan blood to the island.
The final story of the first P.R.O.B.E. anthology has Giles stating as a 'known fact' among the occoult community that the stones currently at Stonehenge are not the 'authentic' ones; the originals were removed at some point and replaced with modern replicas in order to prevent evil ceremonies from being held there again, but no record remained why. (Turns out it was the Yssgaroth.)

The hilarious word here is modern. Those stones errected 2,500 years ago? THOSE are the "modern replicas". (Relatively modern.) So a Stonehenge -did- exist 5K years ago when the site was originally errected... but it used different stones. (Those stones were removed to make the portal hard to access some time prior to Geoffrey of Monmouth's history beginning. We never actually find out if they were destroyed.)

Theorizing: Multiple sets of stones were brought over from Africa to construct multiple stone circles at the same time 5k+ years ago by the 'giants'.  2,500 years ago Merlin took the non-corrupted stones from the Irish circle and put them on the site of the Durrington Henge to make it harder to use for Yssgaroth ceremonies.

It worked too -- when cultists try to contact the Yssgaroth in the P.R.O.B.E. anthology's finale they basically have to bypass the stones and use the site despite them, counting on an alignment of etc etc etc... to make up the difference.

I hope that helps!