You have to duplicate both the main comp and all of the subcomps. Then replace the orig subcomps with your new duplicated subcomps in your new master comp. A quick shortcut for that is to select the orig subcomp layer in the timeline, then in the project window select the new subcomp and drag and drop that onto the orig subcomp that you have selected while holding down the option button (I think it’s the option button, but I’m not at my work computer. Might be the control button.)
Or just duplicate the entire project and import it into the working project. That might be easier.
System Setup (for a more detailed list, see my profile)
HARDWARE
Mac Pro 2 x 3 GHz Quad-Core Intel Xeon
9GB Memory
Two 16x SuperDrives
Dual-channel 2Gb Fibre Channel PCI Express card
Apple Cinema HD Display (23″ flat panel)
ATI Radeon X1900 XT Graphics Card
AJA Kona LHe SD/HD capture card
Apple Xserve Raid 5.6TB
SOFTWARE
Mac OS X 10.4.11
Final Cut Pro Studio 2
After Effects CS3
Photoshop CS3
Illustrator CS3
Boris Continuum 5
Sapphire Plug Ins
Roxio Toast
Digital Anarchy Anarchist Suite
ParticleIllusion 3.0
Trapcode
Zaxwerks