On the 6th June, Microsoft released an update to Media Center 2004 which is now availiable through the Windows Update site. The fix is specifically designed to correct an issue where Media Center can delete some of your recorded television shows, should the recording drive be changed.
The deletion of shows will occur if the new drive is of a smaller size than the original and Media Center is set to keep all shows until space is needed. If you did not select save after switching to the new drive before selecting the old one again, Media Center will use the new drive size and delete any shows on the original drive required to ensure there is space to record.