As for the original Alphans having been replaced by Skrulls...

Spoilers...
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They weren't returned with the other replaced heroes, villains, etc at the end of Secret Invasion...Even Mockingbird (a character who died a real death years ago, and whose soul was trapped in hell) was there...What's up with that?! Omega were not shown playing any part in fighting off the "invasion" and Alpha remains dead...

Dana