Wow! How did you get a picture of the inside of our side hatches??? You may guess from this that I have the same problem. I don't fancy a total replacement of the liners at this stage so am going down a slightly different route.
The basic problem that I have is that the cill of the hatch opening is at right angles to the side of the boat. But since the side iof the boat is not upright - it slopes slightly inwards bottom to top - the cill area is a water trap. A decent varnish along the bottom of the liner should be able to deal with the occasional splash but if it is sitting in water for significant periods......
Step 1 - get rid of the water trap. I've stripped the paint off the cills and primed the metal. Then I equipped myself with a couple of tins of car body filler (two-part epoxy or similar) and gradually build up a slope on the cill, inside to outside so that any water which gets in will be shed outwards rather than sitting on the cill. Remember to allow for the closure of the metal hatch - I had to stop the slope slightly in from the outboard edge since the metal hatches are a tight fit. Then sand, prime and paint to match the boat.
Step 2 - the bottom of the timber liner now fouls the newly created slope. I've tried various methods of creating a small bevel on the bottom edge of the timber liner but it is hard work removing wood evenly. I've got the promise of the lend of a powered router which. I am assured, will remove an even amount. Even if I take off a square section, the gap will be hidden by the framimg around the hatch opening.
Step 3 - thoroughly clean down/sand the bottom edge and door faces, prime and paint. I doubt that you will get away with cleaning up the existing. It looks as bad as ours did so we used paint to provide a contrast and that will have a stencil/transfer added so that it looks like a feature rather than a repair.
[Remember, when you add the new liners, to check that they clear each other as you open the hatches - I'm having difficulties with edges catching each other as the first door opens.]