The question about how the fanfics were created is because of the way they are handled by the Kobo devices. As you can see, when the device is unplugged, any new books are processed. This is to add details about them to the internal database. The database is used for the library list and lots of other things. Unfortunately, this can go wrong if there are problems in the books. Sometimes the processing will hang and the only way out is what you are doing. Other times, it appears to work, the home screen is displayed, but the books are not in the library.
So, if the books are error free, they should be processed OK. And how likely they are to have errors depends on the source. As you are talking about fanfic, if you use FanFictionDownloader (FFDL), then I would be surprised if there were any problems. But, other sources might not be as good. The Kobo firmware can be picky about the books it will process and display. Or maybe I should say it is unforgiving about erros. JSWolf's suggestion of checking for errors using epubcheck against is a good. But, if you haven't already used it, then it takes a little setting up. You could use the error checking in the calibre editor. It is there as part of calibre and doesn't need anything extra. I would be surprised if something passed it's errors and wasn't processed by the Kobo firmware.
Testing on another PC is also a good idea. If this is a new device, it might be faulty. If you have the same errors with a second PC, then maybe it is an issue with the device and need to be replaced. Also, a factory reset can fix some strange problems like this. You would need to reload all your books afterwards, but if the problems go away, that would be worth it.
Oh, 80 books is nothing. I have about 1400 on my H2O. There are people complaining they have trouble getting several thousand on their devices.
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