You could download the ISPConfig tar.gz, extract it and go to the install folder. Run setup.php and answer "reconfigure services" with "yes". So all service config files, including ftp, are rewritten. Be sure you check that your pureftpd version is the correct one (apt-get install pure-ftpd-mysql) and not the one without mysql support
I don't know what you mean with "all your settings". You will loose all changes in config files that are altered by ISPConfig setup.