Hi Joe,
Do you get the same problem if you log off and re-logon to open the report? It could be you had a copy of the original cached. Also, did you try the same workflow in the Webi Rich Client or Java viewer just to verify the new datasource works? The error suggests the universe cannot be found, but its more likely a problem with changing the doc while it is opened in different sessions.
Also the version you are working on could play a factor. What SP and Patch level are you using?
Dan