The flies are there most likely because it is just a resting place. Your Arborvitae are beginning to show their age. It is natural to have browning older needles on the interior. If your plants have not been fertilized recently, feeding them in the spring of year when actively growing will give them a boost. Watering older plants during hot dry weather and not just during a drought will also aid in recovery. Evergreens planted closely together as is often done to create a barrier or hedge will increase the amount of browning as they grow together and lessen sunlight.