Magnesite is a natural material that is an off-white (dairy creamer) color and has granules that are 2mm or smaller. It is soft so the larger granules should not pose any problem. (The "B" in Bear Tooth Woods in the photo is 3mm high.) Sold in a 10 gram bottle that should finish many pens depending, of course, on how large of a void is filled.
I like to use a small screw driver to transfer the material to the void, fill the void with the material then use thin CA glue to secure. You can use a piece of paper under your pen to catch excess material that may slide off the pen. Before turning, make sure the CA glue has FULLY cured.