OK, so you right-click on a filing tray, select "Move selected Entry" from the pop-up menu, and the next 'popup' screen shows that filing tray highlighted..now, don't select a new destination for it, just click "MOVE", and voilla! It's gone!
If you want to get it back, open hierarch.pm, find that filing tray..
it will look something like this... (assume the tray is called "mystuff" ).
1,2,"12345678:mystuff","12345678:mystuff","mystuff"
Yep, the tray is tucked nicely inside itself.. Pegasus considers that to be roughly the same as "dividing by zero..", but says to itself "I'm not falling for that", side steps it and moves on..
Close Pegasus (if not already), then edit that line in hierarch.pm to something like:
1,2,"12345678:mystuff","xxxxxxxx:My mailbox","mystuff"
(where xxxxxxxx is the address shown for "My Mailbox" at the top of the hierarch.pm file)
Open Pegasus, and your "mystuff" tray (and all its contents) should be back, now in the folder tree down one level from the main mailbox listing.
What might be handy is during a bug fix, maybe check the destination during a move to make sure what is being moved isn't being moved into itself..