Resonating trussrod. How to fix it?

Bones

When I install a truss rod on a new guitar I use a small amount of RTV. Just a few small dots of it and never had one rattle. Never tried this but you might try RTV thru the holes under the fret dots but mask off the wood where you want to glue the dot back in. RTV cures soft and rubbery so my thinking is it will damp out any resonance.

Jehu

I would trust your luthier rather than a bunch of people on an Internet forum (no offense, guys!!).

If you don't trust your luthier, time to find a new luthier.