This error occurred twice in WinSCP. I love the program but this functionality is coded poorly and has affected a relationship with one of my clients.
I open a php file for editing in WinSCP and if after I save my changes and the new file upload fails/aborts/timeouts, WinSCP will shut down unexpectedly and when I reload the application my file is deleted! Needless to say, my client is angrily seeking a backup of the file now. Not good for business.