Who are you kidding? There is zero collaboration between MSFT and RIMM. Microsoft turned their lawyers on RIM and demanded payment for patent infringement. RIM caved.
Easy to understand RIM can not handle yet another ongoing patent lawsuit. You can easily find all this.
Changing internal file systems, integrating it, and rewriting all the code using it at this stage of development is impossible; so RIM is already using it, therefore Microsoft can demand as much as they want. And they know how much cash RIM has.