Windows System Restore will only change system files, settings and programs. It won't touch personal files - your own documents, photos, etc. Since Duplicate Cleaner is designed for your own files, and not system files, it is best not to rely on System restore to back up your documents - you should back it up independently.
More information here from Microsoft
http://windows.microsoft.com/en-gb/windows-vista/what-types-of-files-does-system-restore-change
More information on backing up your files here.