I don't think re-dipping will harm the diamond. The diamonds also do not need to be removed. The plating material will only adhere to the metal so no harm is done to the setting.
One time, a few days after I had my yellow gold ring dipped I noticed that it looked really scratched. I took it back, and they buffed and re-dipped it. It looks brand new! I usually drop my rings off and pick them back up within 30 minutes, so I have never worried about diamonds being switched.