No, you won't have to unpair your AirPods from your iPhone to use AirFly. When you pair the AirFly to the AirPods, they will disconnect
from the Bluetooth on your iPhone, but they will not unpair
. Once you're finished using AirFly, simply go into your iPhone Settings, tap Bluetooth, then tap AirPods, and they'll connect without having to pair them again.
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