Your master part should be stamped as a Revision to protect it. Ideally it would have some kind of part number - but per best practices it must at least have a unique file name.
I don't have all the answers, but that is another thing for me to test...
Here is an example to think about.
Disappointing that if you look at Where Used or Contains on the master multibody part 3-11-14.SLDPRT file it has nothing. However, on the plus side, if you change the state on one of the parts or on the assy the master part is included. So I think you send them all through the workflow to released state at the same time as the drawings. Also any time you go to check out one of the children the master part shows up as something you can also check out.
As a general rule we do not allow this type of workflow.
The Designers / Engineers that what to use this methodology assume that it gives them more control and freedom but it really make for greater risk of unintended changes due to changes in the parent part. In fact, you need to protect that parent part even more so. It needs to be revision controlled and requires strict checking after any change to ensure that only the parts (bodies) that were intended to be changed are and that those parts are being released.
Tim, Thanks for you input. I'm starting to come around to your way. It's a cool design tool but could cause too much room for error. After designing this way do you have a best practice for then right as the designs seems pretty solid to break the ties and make the 'saved out body parts' be standalone with all the features included? I notice under references there's a check box that says include all feature if links are broken (or something like that) but then when you break the links nothing like what is implied happens. it's just a dummy part now as if it's been iges'd in. Anyway, thanks.