"Everything" is a "virtual collection", and is basically just a canned query for "show me all clips that aren't in the trash can".
You've also got "today", "this week", etc.. They're all in the virtual collection folder, and are documented here:
http://www.thornsoft.com/HTML_help/7/ue ... ctions.htm
When you're looking at any virtual collection, it will show a column that shows which collection any given clip actually resides in. That may shed light on where they all went. See if that is helpful at all.