View them as seperate worlds. In the world of GCEA, they are all dead. Authorities would have found the bodies of Jacob, Brettles Lucian etc and figured out that they died fighting the battle. They'd be remembered as heroes. Joseph on the other hand, wouldn't have been found until someone went through Victory Road, which is somewhat sad, in that people wouldn't know what he died for.
In a nearby world (where BB and TY are), there is a Jacob (and maybe a Joseph, Brettles and Lucian) and the next day in that world, Jacob from DE woke up in the body of Jacob in the BB/TY world, where the Shadow Crisis didn't happen. Joseph could do the same thing.
I know Lucian didn't do it that simply, though I can't say details until @
Rival Max posts his story.
I am pretty certain Brettles would have stayed with Chime (JD referred to him as Chairm at first by accident, so I have called him that. Turns out his name is Chime).
As for Joseph, feel free to do what you want with him. You could have him wake up in the same world as Jacob, BB and TY, or he might wake up elsewhere. Or he could stay with Chime.
As for Clea, she is tricky. Depending on what Xanthe wants to do, she could have been given the same opportunity by Arceus. Or she might not because of the timing of her death. Which means that the soul of Clea from DE could be gone.
Hope that makes a little sense.
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