Hi David,
During upgrades we update skins in the /Data/skins folder which is the catalog where skins are copied from when new sites are created (though we sometimes add new ones and may not always update very old ones). But we never touch any skins in the /Data/Sites/[SiteID]/skins folder which is where the skins used by the site are.
We keep a sticky thread about important skin changes in our design forum, so what you need to do is check that thread before and/or after upgrades and apply any needed changes to your own skins to bring them up to date.
In version 2.3.7.6 we added a bunch of new skins designed with artisteer 3.1 in /Data/skins and we moved most of the older skins into a separate extra-skins.zip download so the older ones did not get updated unless you get them from the extra-skins.zip on our codeplex download page.
Best,
Joe