Calibre 0.9.2
Calibre Companion 2.3
I connected my Nexus 7 with 2028 books to calibre in 1 minute 17 seconds. The time that calibre took to compare the metadata was negligible. Previously the time was north of 30 seconds. Very quick.
I deleted all 2028 books and it took 19 minutes and 21 seconds. Also very quick.
I sent all 2028 books back to device. It took 3 minutes for calibre to queue the job and send it to the jobs menu. Then another 3 minutes before it actually started to send books to CC. Total time recorded by calibre in the jobs queue 30 minutes and 47 seconds. Fair time, along the lines of what I would expect.
Once it started the actual physical transfer of the books it sent 1 book every .82 seconds.