While not Ideal, you can just varnish over the thin spots. as long as you maitain a good thick layer of varnish you should not have problems.

Ideally, you should add a thin coat of your normal epoxy, just squeegee it over the area. allow it to cure overnight then wash off any amine blush and sand (lightly) to give the varnish someting to stick to.

you will have to use your judgement as to whether or not you need to add more epoxy. I would only do it if you have really sanded to the wood, if it is still coated with epoxy you should be ok. You may have sanded through the fiberglass cloth (if you used it on your CLC deck) which again isn't Ideal but is ok if it is on the deck and not highly stressed.