Pic would help...
Being a learner, i likes a rest... stuck one on the GSR200, often find myself using the end of the fret board on the SR600 as the pickup are quite tall...
The wax idea sounds like a cunning plan, where a replacement pick guard wont fix...
Are these the Hardware store, Homebase Furniture scratch type crayon?
Maybe a cocktail stick snipped to go below the surface to take up most of the hole, with a crayon topping...