On each jira upgrade the installer script will override all files from JIRA_INSTALL even if these do contain essential configuration settings:
/bin/setenv.sh (or bat) - which contains how much memory jira needs, ESSENTIAL!!!
/config/server.xml - web server config, essential
/jre/lib/security/cacerts - trusted CA certs without this, ALL SSL connections like LDAPS, POP3S, IMAPS will be broken after the upgrade.

The upgrade should just upgrade jira. Also because it does archive current install directory it takes too much time. The logs directory shouldn't be archived, it should just be kept.