Before I attempt to install the new version over the old version via package upload, will this method overwrite any settings or styles of the existing template? I need a definitive answer on this.
JB Templates not upgrading via Install From Web has been a persistant problem on both Redhat and Debian distro servers, and I don't believe it related to my server config, IE today I have successfully updated via install from web T2, ZenTools, ZenKit, Zen Social, and several other JB extensions on this site with no problems.
Requesting administrative access to a site should be a last resort. You did not even make an attempt to troubleshoot what those messages and warnings might mean.