Customized Templates Overwritten on Upgrade
When upgrading VaultWiki under XenForo, any templates owned by VaultWiki that have been customized in a custom style will no longer be customized after upgrade.
Fixed in the next release. VaultWiki's XenForo upgrade script will use a manifest file to track which templates are still included in the product, and will now only remove existing templates that are not on this list. In previous releases, the upgrade script used the vBulletin behavior of removing all VaultWiki-owned master-templates prior to upgrade, then reinstalling them all during the upgrade. However, in XenForo this dissociated customizations from the new master versions of the templates, since customizations are parented based on primary ID rather than by template name (in vBulletin, parenting is only implied by template name). It is unclear whether this dissociation is new behavior due to changes in the XenForo core since 1.1, or whether this has always been the case.
In the mean time this is "patched" for the current release by disabling VaultWiki's ability to remove stale templates during the upgrade process.