Mark,
I attended the BI 4.1 Partners workshop last week in Vancouver. This is what I was told, as long all you customization is proper configured and located in the \Tomcat6\webapps\BOE\WEB-INF\config\custom\ folder, it will retain. I am waiting for my BI 4.1 ramp-up to extensively test these features.
The same issues is their when you do in-place upgrade of XI 3.1 to SP6. XI 3.1 SP6 also now upgrades to Tomcat7 but the customization retention is a little more complicated.
Regards,
Ajay Gupta