you probably set it up incorrectly. and it didnt remove the files. nothing ever gets deleted. if you set it to MOVE mode it cleans OUT your folder by moving unused files into another folder. Ify ou set it toe COPY mode it builds a new site in a new folder only containing the files needed. There is no way it deleted any of your files. It never deletes any files. In only moves them OR copys them depending on the settings.