I had something similar when I had a failed upgrade on a vCloud, going from vCenter 5.0 to 5.1, the upgrade failed, and as a work around, I build a new windows host, ran the 5.1 upgrade on the windows host and pointed at the (non-local) SQL DB server. Everything seemed to go well until we had to reconnect vCD to vCenter, at that point we got the UUID error. Doing some reasearch, we found the UUID in the local ADAM database on the vCenter as well as in the C:\ProgramData\VMware\VMware VirtualCente\instance.cfg file. It appears to only be referenced once or twice in the vCD SQL DB, so we decided to modify the vCD DB to have the new corrected value for the vCenter UUID instead of the other way around. It seems to have worked out well. The UUID is stored in the vCD DB under: select * from dbo.virtual_center . You have to be careful when you replace the vCenter with a fresh install, the ADAM DB stores a number of things, such as Linked mode data, License information, Roles & Permissions, Most of which doesn't appear to be an issue when rebuilding from scratch like this as long as your not in linked mode. I am not an expert on the ADAM DB or vCenter upgrades, so take all of this advice on your own risk, but hopefully it helps if any of you get stuck.
See these for more details.
http://kb.vmware.com/selfservice/microsites/search.do?language=en_US&cmd=displayKC&externalId=101748...
http://www.yellow-bricks.com/2010/08/09/standby-vcenter-server-for-disaster-recovery/
-Brian Smith - VMware VCDX - http://bsmith9999.com