Ah, that's a huge pain in the butt. Last I checked, any discrepancies in the file structure will result in FCP's Log and Transfer not being able to see or convert the media.
Andreas Kiel and some other computer experts in here know how to reconstruct files like a LASTCLIP.txt file for a P2 card, but I don't know if the same can be done for AVCHD MTS structures.
Voltaic can access the MTS files directly and convert them, but it's slooooow. I haven't used Clipwrap.
www.derekmok.com