I guess, at worst, you could replace the bad boards or even 'cap' them. I know this will not sit well with you for the obvious reasons but until you find a definite solution, leave them alone.
One other thing I though of ... ARE the bottom 'ends' stained? If no one got up under there, then the rodents will chew a bit until they don't like the taste. Use a mirror if you're unable to get a good look at the ends of the siding that are closest to the ground. Also, you didn't mention anything about calling the manufacturer. I would to that but first I'd make sure the ends have a real good coat of stain. You know, the ends will soak up more stain then the sides. Even if you know there's a good coat of stain on the ends, go ahead and put on another heavy coat. Let me know about this and the manufacturer on the next go-around. This is a doozy!