There are various issues to remember when doing major upgrade version of any sort, however the theme layer is pretty straight forward. With that said, we make a few assumptions:

1. You haven't drastically altered the html
2. You don't have any insanity in the template.php (i.e. overridden views, etc)
3. You actually utilized the zen classes/ids

As I said, this is pretty straight forward, but it's a bit of grunt work. Moving from one version to the next is simply checking the following:

1. find all instances of path_to_subtheme() and change them to path_to_theme()
2. replace template.php with the STARTERKIT template.php and update it to match your theme name (as you would if you were creating a new zen subtheme)
3. replace theme-settings.php with STARTERKIT's theme-settings.php. Again update per the typical subtheming requirements.
4. manually compare line for line your page.tpl.php files vs zen/zen/page.tpl.php. The items that have definitely changed are fairly obvious doing this, but the big item is the language definition at the top of the page and $sidebar_left -> $left and $sidebar_right -> $right. By and large your html should look very similar. For the most part you won't even need to replace most of the html (though some of the new selectors are very useful).

Again, as I said, this is pretty straight forward, but it's a lot of grunt work. If you've over-ridden views, it's completely different in D6, so you'll need to migrate to views tpl files per typical views 2.x styling.