Great question! SharePoint kind of stores forms in a database, but the Qdabra Database Accelerator (DBXL) stores them in the database and ALSO allows you to define a mapping between the XML and other relational tables so that you can shred the actual data into the SQL tables and then run reports on it later. This is the core feature, and then there are also other features such as locking, searching, and versioning that you can learn about on the product page: http://www.qdabra.com/products.aspx
So, does the FileNet application use a SQL database as it's storage medium? If so, you should be able to use DBXL to shred the forms into the database and use a mechanism on the client side to associate each form with the corresponding entity in FileNet.
Matt Faus / Microsoft InfoPath MVPQdabra® Software / Streamline data gathering to turn process into knowledge