I had the same problem a few days ago when I updated from 4.0.2 to 4.0.3. During the update, the script tried to keep my changes and merge it into the updated template.
All changes that couldn't be merged appeared in the admin panel after my update, with the option to show where my customized template is different to the old and the new default one, and an option to revert the changes or edit the template to insert my changes into the new template.
All color changes that were made with the stylevars didn't cause any problems at all, these were all kept. Just the manual changes in additional.css or any other templates have to be checked after updating.
I found that solution very easy to use and re-doing the template changes were faster than I expected this way.
Hope this helps a little..
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