WordPress v1.2.1 has been released and this site has now been updated.
Updating was achieve using the ebuild now attached to the security bug in the gentoo bugzilla, and webapp-config performed as expected and merged in my changes to the colourscheme sucessfully.
Hmm.. Yes Richard it seems the stylesheet did get reverted. Doing a diff between the old and new isn’t fun. gnu diff just see’s the changes as one big remove of the old and insert of the new!