Most people i have talked to use UXStyle Core for applying unsigned themes, it does not modify or patch the system files but runs an independent service that allow unsigned themes to run.
I have linked a tutorial although it is written for Windows Seven it is the same for Vista; Enabling Custom Themes - Windows 7 - Windows 7 Forums
Although it says it is beta i know a lot of people who have been using it without incident since the early days of Seven,
If you want to try & remove your present method of patching which you will have to do before using UXStyle Core have a look at the Q&A at the end of the tutorial
Hope this helps could stop future update issues & you should be able to reinstall the update you removed