When you select Analyze Source Files in the Distributed Files tab, the Deployment Utility should go through every file in the workspace and update its information. I am not sure why this is not happening, could you post screenshots or a video of what is happening and what you would expect instead? Do you have a simple case that reproduces the problem?
Also, TestStand is compatible with different versions of LabVIEW (which I assume you are using to develop with NI-FGEN), updating to a newer version of TestStand should not affect your ability to run code modules generated in LabVIEW using NI-FGEN. For more specific information about what versions of TestStand and LabVIEW are compatible see: http://www.ni.com/teststand/product_lifecycle/
Hope this helps,
I am happy to hear that the problem has been resolved. If you need any more help don't hesitate to ask!