Darkening is only a clue to the damage. Usually if the wood is changing color it's gotten wet and that causes rot. You'll need to remove the glass at the damage area and see if the ply is rotted or not. If it is the rot has to be removed along with the ply and then replaced.
If not, you might be able to bleach out the color change with oxalic acid, get from a full service pharmacy, then redo the glass. Getting a perfect color match is at best difficult since the wood changes color under the epoxy/glass with UV exposure and the new wood hasn't that damage.