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 them up independently.
More information is here from Microsoft
http://windows.microsoft.com/en-gb/windows-vista/what-types-of-files-does-system-restore-change