We live in a log home, tucked into the middle of 34 acres of hardwood forest. Carpenter bees are literally eating us out of house and home. After 14 years, we have tried everything imaginable to repel and or kill them. We have surrendered that battle.
Now I am simply looking for something to fill the holes that will replace the wood that was bored out. Since the bee holes can be up to 2 feet long, I need something that can be injected into each hole and will solidify and harden to restore strength to the wood.
Rather than assume that you have compromised the structural integrity of the wood, you might want to have someone inspect it to see if you have to just fill in the surfaces cosmetically or if you need to fill in the galleries since there is a structural concern. If it is just cosmetic, you can use a putty on the surface and then stain with a stain to match the logs. Test a patch to make sure that the color is right. If you have to fill in the galleries, you might want to consider inject a two part epoxy leaving a dimple at the surface. When dry, fill in the dimple with the wood putty and stain it. An alternative filler would be plastic auto body filler using a turkey fryer "injector."