3.x requires a new database schema for the CMS and Auditing databases. What we did was
1. Completely uninstall XI r2 then install 3.1 pointing to the new database schema. (If your FileStore is on the same server as BOE, be sure to back it up first.)
2. If the FileStore is on the same server as BOE, copy it into the correct folder in the new install.
3. If your FileStore is on the network, update the configuration of the Input and Output file repositories to point to the correct location. The reason for this is that some of this information is stored in the registry.
3. In the CCM, stop the SIA and go to Configuration tab of its Properties. When you click on the "Specify" tab for the CMS databse, you get the option to "Copy data from another Data Source". Use that to copy the data from your old CMS database to the new one. This will take a while and there is a validation that will run afterward that makes sure that all of the objects are still in the FileStore.
I did this in the Dev, QA, and Production environments with not problems at any point.
-Dell
A computer only does what you actually told it to do - not what you thought you told it to do.