Upgrade woes

Well the upgrade seems borked somehow - the comment links are broken. I thought I would use the refresh template option to restore the templates back to the factory default (and then edit my changes back in again but when I try to use the Refresh Template option I get the message "Error creating new template: Template with the same name already exists in this blog."
Unfortunately it doesn't mention which template has the problem and I can't see any of the templates that it is trying to replace. A bit of troubleshooting guidance to mention which template would not have gone amiss in the software.
In the end I had to use the "Delete all templates" option, but it was able to backup the templates for me. Doing the refresh option did not work.