There are three specific files that are intended to be permanent files that should NOT be deleted upon uninstall, re-install, or upgrade of SmarterMail.
freshclam.conf - this file is now CRITICAL to ClamSup.
clamd.conf - this file is intended to make permanent changes to ClamAV.
local.cf - this file is the proper place to put any custom SpamAssassin rules, etc.
None of the above files should be touched if present (just like other configuration files).
Please change the installer to leave these files alone unless they are not present (a brand new install).