Just came up with the same issue. Shutdown computer with document open and checked reopen windows on restart box. On restart a blank sheet loaded. On closing the window and reopening document it reappeared. Hadn’t made any unsaved edits before shutting down so no data loss but scary.
OS X 10.10.1
FoldingText 2.0.2 (738)
Ask to keep changes when closing documents (yes)
Close windows when quitting an app (no)
File affected is in a Dropbox folder.
Automation apps: Keyboard Maestro, Bartender, Alfred, Hazel, TextExpander
Safari, Mail, Excel, Messenger, Preview all reopened at the same time.