Most scratches and gouges in polyethylene kayaks represent only cosmetic injury and don't really substantially weaken the boat.
If you feel that the damage is sufficient to compromise the strength of the hull thermal welding is probably your best bet. This requires some scrap polyethylene material, a heat source, and some flat metal implement like a putty knife or flat head screwdriver. In addition you might need an inexpensive scraping implement to "gutter out" the gouge a bit and smooth any rough edges. A good heat gun or a propane torch or a purpose designed plastic welder (as sold by Harbor Freight) can be used as a heat source. You could check with Necky to see if they can provide you with some color-matched polyethylene welding rod.
There are a number of DIY explanatory videos on youtube that demonstrate the process. Most of these describe repair of through-and-through cracks but the method is the same.
Here is one:
and here is another:
G Flex epoxy is one of the few adhesives with will bond reasonably well to polyethylene if used exactly according to directions:
Recreational Kayak Paddle
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