After setting up the Tivo Series 3, a few recordings were missing from my Series 2 Tivo. It took me half a day to realize it, but clicking through the setup on the new box had managed to work through the menu to delete recordings on the old one! Tivo boxes and remotes are all interchangeable by default, hence the crosstalk.
There is a procedure to uniquely pair the remote to the Tivo which you could do on the older Tivo before setting up the new one. Alternately, you can cover the sensor in the middle of the old unit until the remote is paired.
