You are right -- 8000 books is beyond what we thought we were dealing with. However, you are doing it, and DoctorOhh (another MobileRead & CC user) has more than that. IIRC he is up to close to 10,000.
We are happy that CC doesn't fall over dead.
Could you provide the entire debug log? I need to see where CC and calibre were in the sync process.
Had CC finished sending metadata up to calibre? Had it even started sending metadata up to calibre?
One thing you might try: turn off CC's auto-scan for new books. It could be that the scan is (sometimes) taking longer than calibre is willing to wait. Turn it off in settings -> Wireless connection settings.
Another thing: be sure that your phone's main memory is not full. Bad things happen if CC runs out of space for its database.