The symptoms you describe of constantly "updating the software" and no books recognized, even after writing them, and not recognized by Calibre, are exactly what I went through. This seems to be caused by a problem in the Kobo software.
I believe you have to take the SD card out to reload it. There are multiple partitions on the SD card (as you also see in the image), and when it's in the Kobo and connected to a computer, the Kobo only shows the data partition to the computer. I don't recall if the data partition is empty after reloading, but on first restart after re-inserting the SD card, the Kobo goes through some process to initialize things, and the .kobo folder is definitely there on the data partition after it completes. After I checked that, and wrote a book, restarted Kobo (without the "updating" message), reconnecting and still seeing the book, I re-assembled.
It's very easy to open up the N289. Just need to slip something between the top and bottom shells to gently pop the plastic tabs that hold them together. Here's a video of a guy doing it completely by hand (no tools), but that didn't work for me, as the bezel was a little "sticky" against the screen, so I slid a thin piece of metal between the pieces (I also heard of someone describing same process, using a plastic card as the pry tool).
https://www.youtube.com/watch?v=nduY8RT1kVQ
Good luck!