Upgrading or re-installing over an existing version
For Automated Installs:
All the code files are overwritten completely. If you have customized "search.pl" or one of the code libraries, then you should save a separate copy of the customized code file and later add your customizations back in.
All the data files - search.realms.txt, settings.txt, templates, etc. - will remain intact. Thus, if you have customized the HTML in your templates, or started building your search realms, then you can still safely upgrade or re-install the search engine with no risk to existing data.
The install process will leave data files intact if a file with the same name already exists. To fully re-install the product, delete data files manually. Then the install process will start you out with default data files (templates, ads, realms, etc.).
For Manual Installs:
Replace the "search.pl" script and all files in the "searchmods" folder.
Replace the files in the "searchdata/templates" folder. If you have customized one of the public templates, like "templates/english/header.htm", then keep it.
Leave the data files in the base "searchdata" folder intact. This includes "ads.xml", "settings.pl", "index_file_1.txt", etc.
"Upgrading or re-installing over an existing version" http://www.xav.com/scripts/search/help/1036.html