I recently had a DVR replaced because of the new HD channels. After installing the new box, all my recorded shows are taking up space on both my DVR's.
I have Multiroom DVR but before I could record separate shows on each DVR.
By any chance,Have you imported schedules of other DVR after getting new box?
When you connect a new box ,it might have asked to import the schedules from either of your boxes.From your issue , i guess you should have imported schedules of your other DVR ,so that both boxes have same schedule and record same shows on both boxes.
Check the schedules on both boxes to confirm