James,
Please provide more information on how your projects are settled. Are they settled to COPA? Do you use Results Analysis?
What is the relationship between the 2 Level 2 WBS elements? Is there a revenue sharing relationship, do you have SD orders involved?
It sounds like you need a reporting solution rather than a functional solution.
You could create 2 projects and use Customer Defined Fields (implemented via a User Exit) to link the 2 projects for reporting. When you need to reassign a project you simply change the Customer Defined Field on the Project definition.
The Customer Defined fields are available in standard PS reports as a selection.
