I recently received a gloss blank that had a couple of very small, but still noticeable, scratches on it. Unfortunately, I didn't discover this until I made some test wraps on the butt and finished over the wraps. It's possible that maybe one of the two scratches might end up under guidewraps (and, therefore, not be a problem), but I doubt both will be that way. Here's the question: Can I do anything to get rid of these scratches? Can I cover over the scratches with a very thin finish--Permagloss maybe? If so, are there any specific guidelines I need to follow?

It won't be a tragedy if I can't fix it, but I'd like to, if at all possible.

You could coat it with permagloss but it will stand out. You might try buffing it with a soft wheel and very very fine compound. But if you overdo this you'll burn your finish and again it will stand out.

Scratches are not uncommon these days. Can't remember the last blank that I got that didn't have a couple.

Try waxing with a good carnuba based wax, without a cleaner.