Did you update to calibre 8+ and were you using the Kobo Touch Extended driver? If so, that driver is now blacklisted since it's functions are now part of the KoboTouch driver. Sadly, the configuration from the KTE driver is not transferred over to the KoboTouch driver and you will need to do so manually.
You can find the KTE configuration file at C:\Users\<username>\AppData\Roaming\calibre\device _drivers_KOBOTOUCHEXTENDED.py.json with the following three lines being of most interest for creating collections:
Code:
"collections_columns": "#finished",
"collections_template": "",
"create_collections": true,