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The database processing requirements and function of the Kobo Nickel User Interface is somewhat picky and will take a long time to process or reject ebook files that it objects to.
There is probably a file or two in your 3000 that Nickel doesn't want to add to the database it uses. It may be some minor issue easily corrected by running the offending file through calibre, if you can find it. Nickel's support of the external uSD card has also been an issue, and is often one of their first troubleshooting questions.
I keep ~7000 ebooks in a hidden folder on my external uSD card, hidden from Nickel. Some of them most likely contain "flaws" that Nickel would object to, and there are many in .pdb that the Kobo supplied readers cannot read. I mostly use KOreader which has no problems with these books.
Luck;
Ken
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