How does that match your theory about epoxy shrinkage?
Seems like if the epoxy shrunk on the newly cured side it would have bulged outward on the top.

I would said that it negates both the wood moisture and glass shrinkage theories. If the wood was sealed and straight why would it warp? It must have taken a unfortunate permanent set . Can you apply a light brace around the hatch underneath to pop it back out? I offered up the consideration of glass shrinkage as a possible consideration . I am sure moisture played the biggest role initially. I have been glassing (both glass and resin)a closed cell foam (xps) that is 1/2 inch thick sheet material, if it sits glassed on one side only for a few days it warps into a concave shape. I have it secured to a flat surface after the initial tack off to minimize distortion. Good luck and I am sure you will come up with a way to fair out the deck let us know how you do it.