I have had good luck with the Waterproof type of automotive body filler. Of course, if you have a large volume to fill, it could be expensive.

Is there something called GOT ROT out there? I heard marine people use it for dead wood on boats where the relpacement of the wood would be tough.

I own a log home, and if I had questions of this sort, I'd call either Permachink or Sashco. Both of these companies specialize in restoring and refinishing log homes. www.permachink.com www.sashco.com
Good luck
jh