Whoa, MSIUpgradeCode= must be the same between the two packages.. MSIProductCode is the one you must generate a new GUID for..
And remember to bump up MSIProductVersion so it's higher than the old package..
A blog post on the topic: http://blogs.vmware.com/thinapp/2010/04/upgrade-a-deployed-thinapp-package-with-the-help-of-msi.html