Imperfections and voids are common in stock blanks and nearly impossible to detect from the surface when the blank is still in the block. The reasons for these hidden surprises are varied and dealing with them is fairly straight forward most of the time. When I began my career I made all my stocks from the blank. Once the barreled action was inlet the exterior came off by any means possible band saw, planes, files and healthy amount of sweat equity. At this point more than a few hours of work had been expended and sometimes you ran into a void or bark pocket that would not clean up in the final shaping no matter how creative you became.
In the early eighties I began to use a pantograph on my own work as well as machined stocks for others in the trade. Over the years I was amazed as to the number of blanks I machined that had significant internal flaws. Most all of these were very small and easy to fill. Only a dozen or so in the forest of blanks I cut revealed voids that made the stock blank unusable. The upside to machining the blank to begin with was these flaws showed up as the stock was machined without the labor of inletting now being potently a wasted effort. This method offered a distinct advantage in avoiding a financial nightmare.
Filling these voids can be done with just pigmented epoxy. I have seen many rifle stocks "fixed" in the manner, its quick and if done well almost looks natural. However my preferred method is to use cut off' pieces from the same blank to fill in these cavities.
I try and leave the shape of the void "as is" but when necessary will trim away any soft or rotting material from the edges of the cavity. Then you need to fashion the plug. The layout and direction of the grain for the plug needs to match the grain in the parent blank as closely as possible. These plugs can then be shaped with a file, chisel or exacto blades to fit into the void. Some of these can be made in minutes, others will take considerably more time. The effort and care spent on fitting these plugs will determine the over all outcome of the repair. Done well the repair will look like a solid pin knot. The plug also needs to be fit deep enough into the void to form a solid bridge that will be deep enough to allow plenty of surface area for the plug to adhere to the parent stock. Some people use Yellow Carpenters or Gorilla glue to secure the plugs in place. I prefer a very good grade of epoxy that is pigmented with brown or black epoxy dye. Apply a liberal amount of epoxy in the cavity and on the plug, drive it place and allow the epoxy to set up overnight.
Care must be taken to cut off the excess wood close to surface of the repair without damaging the plug and then the final filing and sanding can be completed.