If you're just trying to sell it, scarf in a section of 1/4" ply. you can cover the edge with trim, staple the underdeck headliner to the new section and reinstall the trim piece. Disclose it to the new buyer.
If you're looking to keep it or do a proper fix. remove the port lights (rebuild them while you're at it), remove the whole piece of plywood, and replace with a new piece. Mahogany or teak faced 1/4" ply works well and is fairly inexpensive, but you can go with a cheaper face ply and paint like Christian said above. make sure to seal the edge of the new ply exposed to the portlights to prevent this from happening again. When I did the side of my 25+ a few years ago, I used the portlight openings as clamping surfaces. Once the glue (thickened epoxy on mine) cured, I cleaned up the edge of the new ply with a trim router.
Here's one of the threads I posted to with my experience:
(Pictures are of the template and before the recore) Now that the recore on the port side is done, its time to install the new piece of teak plywood. I've thought about vacuum bagging it, but the aft section would be next to impossible to create a seal and I don't think I could line up the...
ericsonyachts.org
There's a few other posts floating around here with some good information as well