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I have been asked to refret a 1953 Guild X-175 jazz archtop. Should be fairly straight forward - the fretboard is in good condition with minor divots, the board isn't bound, existing frets have been filed quite a bit but are pretty much level right now with only about 2 thousands of relief and the truss rod is functional but only snug. The problem is that all of the position markers stand about 10 thousands proud of the board. The markers look to be some sort of pearloid material - I'm pretty sure they are not shell. They seem to be uniformly proud - each fret and on all sides. I have a hard time believing that the board has shrunk back that much (and that evenly). There are some small gaps around the markers but none of them seem to be loose. The markers have some scratches on them that seems to polish out with steel wool.

I'm comfortable refretting this guitar (I'll use HHG on the frets) and the f/b is flat enough that I think I can get by without actually sanding and leveling the board itself. What I plan to do is pull the frets, check the tops of the markers for level and try to adjust that with the truss rod. Refret and level as usual. Should I be worried about the markers

If they're really proud of the board you could remove them, do your refret without having to work around them. Then simply clean up the holes of old glue and reinstall them.

If you don't need to do anything to the fretboard I'd just remove them. You can also make sure that they're snug with this method too

What Dan said. After removing an inlay I would check the thickness of the inlay. If it is thick enough I would reinstall it and just level the board as usual with all the inlays in. If the inlay is too thin, you could remove them all and level the board then reinstall them. If you do this you might want to rout out the pocket that the inlays fit in on the fretboard to get the inlays flush with the fretboard, but just a thousands or so high, then sand them flush.