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One possibility is that you have a corrupted book which Nickel is stumbling on.
As a starting point, have you tried just adding 1 book to see if can process anything. (Depending upon how many books you have add, it might be worth trying this a couple of times, in case you just happen to pick a flaky book). If it can add a single book with no issue, it increases the likelihood that you have a corrupted book file somewhere.
A second option would be to install KSM and Koreader. (See guides within this site). Then connect your Kobo to your computer via KSM (i.e. do not go in to Nickel) add a book and eject. Since Koreader does not use the Nickel database, see if Koreader can see and open the book you have added.
I am sure others here can advise further, but at my basic level, I know those are both steps I have taken in the past when I have encountered an issue with Nickel processing new content.
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