It will then ask "Would you like Novell Filr to back up your current Filr folder".
Choosing "Remove" will remove the local files, and start a new sync with the server.
Choosing "Backup" will rename your Filr folder where files are synced. If the Filr folder is C:\Users\user\Filr, it should rename the existing folder to "Filr (archived)". The desktop will then initiate a new sync and download all of synced files to "C:\Users\user\Filr".