Check out the XP Embedded Image Difference Engine

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The "Image Difference Engine" and "Image Difference Applier" tools help you identify and package only the changed or added files and registry keys. This allows for a field upgrade without having to redeploy a complete Windows XP Embedded with SP2 image.  The tools can help determine and package smaller upgrades, including operating system security updates and hotfixes, configuration changes, third-party application updates, and line-of-business data.

The tool can be downloaded from https://www.microsoftoem.com/ (requires registration), and also the Mobile and Embedded Communications Extranet (requires a partner account).