In this thread I mentioned a problem with a collection being wiped of sideloaded books after connecting to my PC and opening Calibre. I thought it might have been an issue with the Kobo firmware, but it's definitely Calibre-related.
I connected my Libra to my PC and did not open Calibre. I browsed the device on Windows Explorer, and then ejected it. The collection was intact. I then opened Calibre and reconnected the device. After ejecting it, the collection was once again down to just 6 books downloaded from my Kobo account, all sideloaded books gone. I'm not sure if this a Calibre 5.0 issue or an issue with the newly updated Kobo utilities plugin, which is configured to automatically run the page count update check on connecting the reader