So most of the roots are eaten away? If so maybe you could cover with some clear plastic and put in shade for a week or two, then remove covering little by little after that to acclimatise the plant.

No, all of the roots are gone, just a little nubby part left; the plant so far is still green and perky. I cling wrapped the pot with long matchsticks poking out of the dirt, so the wrap won't touch the plant just to keep humidity levels higher. I also placed the plants under my kitchen table. They will be staying indoors for the remainder of the year.

@ Candie - Well, not much I can say here, if the roots have been eaten through. You may want to try coating what root area that remains with a rooting enzyme, and hope for the best. Obviously, if the canopy is too big, then you'll also need to prune it back to compensate for lack of roots.
I find it curious that the squirrels ate completely through the root system. Around here, they just bury nuts in my pots during the season, but never attack the roots.