from faq on discord. it will be moved to web site shortly:
This is due to an older SteamVR update switching tracker roles to “Held in Hand”, which explains why most of the time, your controllers get replaced with one of your leg trackers. No matter the case, this is an extremely simple fix:
:star: –> With your trackers turned on and functional, look at your desktop and find the small SteamVR window that shows all your connected devices. There is an arrow at the top left that you can click to open a little menu. In there, find an option called Manage Vive Trackers . All 3 of your trackers should show up and the roles set to “Held in Hand”. We do not want this. Instead, we set them to either their corresponding body part, or just “disabled” .
Your controllers will no longer replace your trackers after doing this