Hello Luc,
(Assuming that you didn't specifically un-install Hauptwerk first: )
If all of the files and folders were able to be moved successfully by the installer then you shouldn't need to install your organs again (although their caches would need to be regenerated automatically). However, occasionally some sample set files or folders can't be moved, for example because of some incorrect file/folders permissions or attributes within a sample set's files, or if a drive timed out whilst the folders were being moved.
However, even then you shouldn't lose any settings or other data.
If you'd like to send us a diagnostic file (via email or http://www.hauptwerk.com/forms/support/ ) then I could have a look to see what might have happened.