In Calibre, under Preferences > Sending Books to Devices (under Import/Export) check your Metadata Management setting at the top. It should be set to Automatic.
EDIT: Also, you might have to connect your ereader to Calibre twice for the metadata/cover to fully sync. /EDIT
If that doesn't help, you could try the Kobo Utilities plugin:
https://www.mobileread.com/forums/sh...d.php?t=215339
You can add that by right-clicking on Calibre's Preferences button, choosing "Get plugins to enhance Calibre" and searching for it.
Its option to try would be "Update ToC for Selected Books."