In ODK Suitcase, there is a button, right next to “Upload”, named “Reset.” If you hit the “Reset” button rather than the “Upload” button, it deletes all the files on your server with no further “are you really sure you want to delete all of the files on your server?” type of warning message.
Fortunately we discovered this with our test server, not any actual data, but suggest adding some sort of warning/confirmation to this button so that no one accidentally deletes all of their files and data in a single click.