Kindle Oasis - books in memory but not displaying on device

My Oasis rebooted itself last night, and this morning I was presented with a blank screen. All my books had gone. I managed to download most of them again from the Amazon cloud, but some I have sideloaded via Calibre were not there. Through Calibre I can see that they are still showing up in the device memory, but will not display on the Oasis home screen. I have tried:

- restarting the Oasis
- checked that I have selected Downloaded documents, and show All on the main screen
- I have deleted a book from the Oasis memory, then loaded via Calibre (send to device), but it still does not display

Is there a way of forcing the Oasis to rebuild the index (I though the restart would do that)? I am particularly concerned about one book that has a lot of notes I have added, and I'm afraid I might lose these.