May be worth a force restart of your remote:
Press and hold the TV/Control Center button and the Volume Down button at the same time. Hold the buttons down for about 5 seconds, or until the status light on your Apple TV turns off and on again.
Release the buttons. Then wait 5 to 10 seconds for a Connection Lost notification to appear on your TV screen.
Wait while your remote restarts. When the Connected notification appears, you can use your remote.