I lost my apple remote, how do I disable the lost atv remote and reprogam the new one?

Unless you paired the old one (don't bother unless you use othe Apple remotes in teh same room - it just makes AppleTV ignore other remotes) it would just work.

If previously paired hold menu and left arrow keys on new remote TOGETHER for 6 seconds while pointing at AppleTV until you see a 'broken link' icon appear on the screen.