Hmmm Chris - I'm occasionally experiencing a similar issue as regards the video media library listings "disappearing". See the first post in my thread http://forums.digitalspy.co.uk/showthread.php?t=1507344

In my case I have a brand new 1TB hard disk, so I thought it was either that or the recent firmware update to 1.00.15. I also have Mogie's media player/channel editor bundle installed. I don't recall having a problem with deleting files as you are having, but the issue with the library listing disappearing is identical. I've only noticed it when a scheduled recording has apparently overrun. A re-boot of the box re-instates the media library - I assume this is the same for you? Perhaps there is an intermittent bug in the new firmware?