Heh. Well my calibre library is already at 12k+. Let's hope CC won't fall over and die at 20k, which is where I'm pretty sure my library will be at in less than 6 months. Pretty sure the main memory isn't full, but could you please clarify what you mean by main memory? The Galaxy Note's internal memory structure is plain weird since there's the 2GB system storage, then the 11GB or so memory that seems to be what the system sees as USB storage (mnt\sdcard). Do you mean the 2GB internal? Currently all my books are on mnt\ext_sd\Books, which is the actual external SD. calibre's files are in mnt\sdcard, which has 6GB of free space left.
I'm enclosing my log from this evening: the first successful session, with "search folders for new books" on in CC failed sending books halfway, not sure why, since this is maybe only the second time it's happened. The only thing out of SOP for me was the need to autoconvert two books, as you'll see in the log (see line 4184). The second session when CC connected to calibre was done without the "scan for new books" option active; connected at first try so that might be a possible issue.
A method of cancelling the file send in CC, or getting out of it would be a good idea here, since when calibre timed out and stopped on my laptop, CC remained stuck on the file receiving screen; had to force stop the app.
If you look to the very end of the log, you'll see another timeout message while sending. Calibre Companion then crashed on my phone, and when I restarted it, it no longer displays any of the books on my device. This is the second time this week it's happened to me: once on the previous version and now on the current version. I'm not sure what's causing these crashes.

That said, I don't want to be syncing my entire library all over again if I can avoid it.
ETA: Tried syncing CC after crash with calibre wiped out library on device (book files are all intact though). It partially synced (got around 90 books) then failed when sending metadata to calibre with this message:
Code:
'NoneType' object has no attribute 'lpath'
Traceback (most recent call last):
File "site-packages\calibre\gui2\device.py", line 85, in run
File "site-packages\calibre\gui2\device.py", line 476, in _books
File "site-packages\calibre\devices\smart_device_app\driver.py", line 49, in _synchronizer
File "site-packages\calibre\devices\smart_device_app\driver.py", line 1033, in books
File "site-packages\calibre\devices\smart_device_app\driver.py", line 693, in _set_known_metadata
AttributeError: 'NoneType' object has no attribute 'lpath'
Will provide a complete debug log later once this latest sync attempt finishes-- I'm letting it run while I go to bed since it's closer to dawn that I'd like right now.