silicoln sealer is a wonderful substance that i use alot around the house.it is very flexible and is used for windows,bathtubs,and any where else you would otherwise use latex caulk.i think that might work for your purpose but it is very thick so you might have to remove the fretboard,i don't think it would squeeze through the tiny hole you are speaking of.one idea though.what about drilling through your inlays(assuming they are dots)and replacing them after you fill.i don't know if that would work as i am more familiar with silicoln than i am with fretboard work.i am sure someone else would know better than i.i will tell you though next time you caulk your bathtub use silicoln instead of latex as it will not mold like latex will.