The first thing that comes to mind, as you sometimes connect from KOReader, is that you are not letting the Kobo software, called nickel, import the books. The driver reads the database for books on the device. This is populated when you eject the device and nickel looks for new books and imports them into the database. If you only connect from KOReader, that will not happen. I don't think exiting from KOReader back to nickel would trigger the import. There are other ways to do it, but, connecting while running nickel is the best.
The next likely thing is that the database on the device is corrupt. The device may import the books, but, the database does not get updated properly and hence, the next time you connect, the books are not seen. But, if this was the case, I would expect that you would see errors when connecting to calibre and the databases is read. Exactly what you see does depend on how the database is corrupt, so sometimes it calibre does not see the error. But, you can run a full database check with the Kobo Utilities
The last thought is, with the timing of when this happened, it could also be related to issues with firmware version 4.32. That had issues with presenting the book partition to the PC when connecting. These meant that the partition would be loaded read-only when you eject. And that caused a lot of problems, such as what you are seeing. Firmware 4.33 was released earlier in the month and that fixes these problems.
Also, as you are not sending books to the device as kepubs, why are you using the KoboTouchExtended driver? The purpose of this is to transform books to kepubs. There is almost no reason to use it if you are not using kepubs. The built-in KoboTouch driver should be enough.
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