I had this issue in Windows 10 for a while, but can't really remember how I fixed it. I recall updating the drivers for network card from the device manager, reinstalling the bluetooth drivers and updating Windows.
Even though Window allowed me to connect my Xbox One controller now, Elite Dangerous did not detect it.
To fix this I had to do the following in Steam
Turn on Xbox one Controller
Go into Steam and select Library and right click on Elite Dangerous
Select "edit steam controller configuration"( this option will not show if your xbox controller is off)
You will now get new controller window popup.
Select browse configs from the bottom left.
Select Community a choose "Official elite Dangerous Bindings" the one with 15 votes.
Elite detects my controller now and I can change the bindings in the game.