Check out the XP Embedded Image Difference Engine

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).