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On a recent 000-28 build, when I was filing the fret ends, I got a little close to the lacquer finish w/ my file. Consequently, in a few spots, the finish got scraped/chipped down to bare ebony. Not quite sure how to go about fixing this? Whether I should sand, tape off & try spraying more lacquer on...or, sand & brush-on several coats & wait for a good cure before final sand & polish. The low E side is particularly worse than the other...

you can drop fill but allow a few weeks to cure.

You can help avoid that happening in the first place if you remove the tape from the fretboard a couple of times during the finish process and scrape back the edge with a razorblade. In this case, you'll have to drop fill, like John said. It will take a number of applications to build it up.