Looks like the folks on the System Center Essentials product team blog just posted some great information on how to use the UpdatePublisherCert.exe tool to replace the existing System Center Essentials 2007 (SCE 2007) certificate with a new certificate for use with System Center Essentials 2010 (SCE 2010). If you are planning an upgrade any time soon you'll want to give this one a quick read:
Essentials 2010 uses a certificate for signing locally published content. The released version of System Center Essentials 2010 is designed to use an updated type of certificate. Use the UpdatePublisherCert.exe tool to replace the existing certificate with a new certificate.
The UpdatePublisherCert.exe tool performs the following tasks:
1. Save the current policy configuration
2. Uninstall the current policy
3. Delete certificates from the certificate store
4. Delete certificates from the system
5. Reconfigure the policy and generate new certificates
6. Resign all locally published software and update packages.
To continue reading see How to update Essentials certificates
J.C. Hornbeck | System Center Knowledge Engineer