So this is a *complete hack*, and just off the cuff, and presuming you 
tested it and it didn't mangle your scene:  You could select all the 
top-level assemblies and do and export-selected on top of the same file. 
 Sort of using a sledgehammer to do surgery, but if the patient lives....

I use this brute force technique all the time (heck, I have it mapped to a 
marking menu) to clean files up (admittedly they're usually just simple 
models, not complex scenes):  Just last month I got a file form 90+ megs 
down to around 5 using this.  I asked the modeler:  "Did you notice how 
long this scene (with maybe 10k polys in it) took to save?  "yah, it seemed 
a little slower than usual..." 
:)
Gotta love how cruft can slowly just glob up your files over the years...
I've been hit by the same Mental Ray requires plague as well.  Grr....

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