It's a good idea, and in some cases a requirement, to rebuild your wiki when upgrading to a new version of ikiwiki. If you have a lot of different wikis on a system, this can be a pain to do by hand, and it's a good idea to automate it anyway. This Debian package of ikiwiki supports rebuilding wikis on upgrade. The file /etc/ikiwiki/wikilist lists the setup files of wikis to rebuild, as well as the user who owns the wiki. Edit this file and add any wikis you set up.