Arborvitae continue to be stressed from the drought of 2012 with damage such as needle loss occurring yet. They do have the ability to generate new buds if the damage is not extensive. If they are healthy other than just needle loss from winter desiccation, recovery is possible. If the twigs are dead, more than a little damage has occurred. You can prune out dead wood at any time, it is not coming back. When there is damage on several different species, the cause is more likely to be environmental than any disease. Prune out the dead, water in times of drought (late July through August), fertilize in the spring. Field mice eat bark, rabbits will eat bark and needles. damage is at the sol line or above the snow line. Fencing out the rodents or using a repellant can be effective, especially for rabbits.