botched fim r2 portal upgrade
Hooray for conflicting documentation from Microsoft. So I found this handy, simple checklist for upgrading FIM 2010 to R2. The problem is if you follow it you’re probably going to end up with a botched Portal/Service upgrade. Make sure you upgrade SharePoint to 2010 BEFORE you run the installer is the long and short of it. Even though it’s written for a test lab scenario, you are much better off following this guide which totally conflicts with the above mentioned link on TechNet…
Following the later in my other environment made for a smooth upgrade.