There's a bug in the latest release of the EC control panel that incorrectly deletes a Jingle folder if all previous files are deleted while new ones are in the "processing" state. For example, say you have 10 existing jingle files in folder called "B". You upload 10 more jingles to folder "B". Directory listing shows 10 existing files and 10 "processing" files. Mark the 10 old files and delete them. Poof - the "B" folder is deleted, along with the new "processing" files.
If you displayed the EC version number in the control panel, I'd tell you what version it is. But it's the latest installed by TorontoCast, the version with the playlist artwork icons and search function and pagination.