Step 1: Unplug all vive dongles
Step 2: Restart Steamvr so everything VR related is powered off then powered back on.
Step 3: Power on and pair your controllers, since the dongles are unplugged they will bind to your headset Leave them on for the remainder of the steps.
Step 4: Plug in one dongle, and pair the tracker. Since there is only one dongle that doesn't have a device attached, it will bind to this one. Leave the tracker on for the remainder of the steps.
Step 5: Repeat step 4, one dongle and one tracker at a time, leaving them on until you are complete.