I am having the same issue only when I click any button on the apple remote I get 3 blinking light which indicate a pairing issue when I try to pair the remote it will not pair than I go to use the apple remote app and the only buttons that function are the menu and play buttons I can't swipe to move up down left or right are you experiencing this as well
An update: On another thread someone suggested that your Apple TV may have become paired with another remote. We only have one so this didn't seem possible to me, but I tried the suggestion anyway and it worked!
Hold the remote very close to the apple tv. Press the menu and rewind button together and hold for 6 seconds. (My Apple TV gave a single flash after 6 secs.) Lo and behold, the remote works now!
Hope this solves your problem, too. Good luck!