I do this so I can watch a premium or HDTV channel from the cable box without messing with whatever is recording on the Replay's RF input. I just have the 2-99 disabled in my guide, so essentially I have 100-999 are the cable box, and 1002-1099 are RF. It only took a few minutes to create new Replay channels to replace the ones previously recording on 2-99, and any zone based recordings which would have been on the 2-99 now record from 1002-1099 instead. Works just fine this way for me.
But, if you're not keeping it anyway it makes little difference.