There's new BIMinFM thread over on the autodesk discussion groups.
It's a big question. How do you make a master facilities file, when you're starting from models created by different companies.

I guess I sum it up with:
1. Archive the original project in it's current state.
2. Mash all the files together and remove all of the content that you don't need.
3. Replace or modify families as needed for simplicity, clarity, etc.
4. Any small changes discovered or made by the facilities staff can be easily updated in the master.
5. Any renovations shall be archived as their own projects in their final state.
6. Changes made during the renovation should be recreated in your master, reusing the already-cleaned content.

But, still, big question. There is some conversation at the original link. I'd love to read more input from others, though. I'm a bit out of the day-to-day with it, since I moved to the consulting side, I haven't been using Revit as much.