To link the remote again to the box: If your Apple TV remote isn’t working - Apple Support - Internet Archive (second half of the page). Do both steps: the unlinking and then the linking.
[The box would ignore (but acknowledge through the status light) signals from unlinked remotes.]
If the remote battery is depleted: How to replace the battery in your Apple Remote - Apple Support
[If the status light on the box blinks, then it is receiving a signal from the remote, meaning the remote apparently has enough battery power to send a clear signal.]
To reset to factory settings: Reset or restore your Apple TV to its factory settings - Apple Support
Else you can restore this model unit through a computer with USB tethering: Restore your Apple TV - Apple Support
- Use a USB cable that supports data transfer. Some cables may be charging only, or may be functional only with a bundled device.
- Power the Apple TV box at the indicated moment (step 4) with its own power cable, if the model is 3rd or 4th generation (not 2nd generation though!) [5] [6].