The install script deletes the original installation files and starts afresh, including the additional downloaded databases.
The advantage of the updated method is that the latest versions of the Sane Security package scripts are installed. These are now at version 3.7 compared to 2.4 of the original swerts-knudsen files. The default databases to be downloaded have also changed slightly with some being removed. The MSRBL databases have been removed entirely as they haven't been updated since last year, but more choices are available listed in the .conf file to be added as you wish. The .conf file also gives an indication of the risk of false positives from the additional files. Documentation including a ChangeLog will be found in /opt/sanesecurity/doc, and you can also do 'man clamav-unofficial-sigs'
As long as the Sane Security package does not change significantly the install script will also download and install subsequent future versions, albeit that you would loose any manual changes to the .conf file i.e. non-default database choices.