Everyone except for the paragons have died, and has been replaced with alternate versions of themselves.
When you think about it, when everyone died in Part 3 of Crisis, they never came back. Rather Earth Prime doppelgangers, or more like clones replaced them. This is evident as they literally had new memories.
When John "restored" their memories, he actually just pulled the memeories of their late dopplegangers and gave it to the Earth Prime versions.
The Earth prime versions of the charactsers have lived separate lives to the ones pre crisis. Think lf it like what happened in Arrow.
When Laurel died, she was replaced with an evil doppelganger from Earth 2. This is essentially what happened, but imagine if Earth 2 Laurel (Aka Black Siren) had the memories of Earth 1 Laurel.
So, everyone died except the paragons. And the Paragons are in denial about this since there has been no proof they come from another Earth.