I have over 7000 books on my AuraHD, but I keep them away from Kobo's processing and they are available right away. Also, a number of the books and documents that I read on my AuraHD would be rejected by the Kobo processing and hang-up the procedure. If I wanted to read them using the stock reading software, I would have to convert some to a format that Kobo uses, and some, that are in an included format already, I would have to find out what the Kobo Nickel processing is objecting to and fix it. There is probably a few of your 2000 that Nickel is rejecting and that can make it take a very long time indeed.
If you can live without the stats and Kobo "Rewards" You might want to consider adding an
Alternative Reader and have calibre place your books into a Hidden folder on your device.
(See the note at the bottom of that post)
Luck;
Ken