If EBS 2008 is still in the middle of installation, I would advice to simply restart the EBS installation.
Since the SBS2003's schema is updated now it shouldn't be a problem anymore.
(You did run the EBS preparation & planning wizard right ?
http://www.microsoft.com/downloads/details.aspx?FamilyID=13e06404-46a9-421d-8147-0e0a4ace9601&displaylang=en)