Be gentle
If you are stripping the stock with some type of varnish/paint remover use it gently on the checkering. I use an "extra soft" tooth brush. Whatever finish you are using thin it down with the appropriate solvent at least 50-50. I found that finishing the checkering last, i.e. after the rest of the stock has had the last coat applied, works best. I use an extra soft tooth brush to apply the finish. Don't goop it on. Gently brush in the direction of the checkering cuts, alternating between the two. Wipe off whatever splashes onto the finished and dry stock around the checkering
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It's a pain but keep in mind a few goals:
1. Remove all the goo from the old finish
2. Don't pile more goo in when applying the new finish
3. Be gentle. Checkering points break easily, especially old ones.
4. Be careful sanding and applying coats on the main stock near the checkering patterns.