Comment 13 for bug 1523291

12000 books? Exactly how big is the database? For about 2000 books, I'm at about 85MB. Six times that puts it over 400MB. Maybe it us something related to the size.

You can test the factory reset safely if you take a full copy of the user partition from the device. After that, do the factory reset and test with a smaller number of books. Then you can decide whether to restore the saved data or start again. If you do this, make sure you take the SD card out. If it has most of your books, you don't want to have them processed into the library before doing the tests.

Another test is to connect without the card. The database gets opened twice, once for the main memory and once for the card. I would need to see a debug log to work out which it was. They shouldn't be different, but there is a chance that the the first open has left something in a bad state.

And have you tried another machine? Checking with an older iMac would help to see if it was this version of El Capitan. A Windows or Linux machine would help to see if it was the device.

Also, trying immediately after rebooting the iMac and the ereader might give the best chance of everything working.