I had a similar problem today. I just finished reading a book and had put the kobo away. At some moment, I registered a movement from the corner of my eye: The kobo had switched from the standby screen (cover of the next book in the carousel) to the carousel, only the carousel was half empty and many of the loaded books were nowhere to be seen.
Calibre has an error communicating with the device.
I was on 1.9.17 and I am now reading up on what the last firmware is all about. Then I may take the risk of upgrading and going through the hassle of setting everything up again (good bye, reading statistics, I hardly looked at you anyway in the last months).