Thanks for your response, davidfor.
It's been a few years since I created the collections and I (incorrectly) assumed that I had used the Kobo Utilities plugin. I double-checked, however, and I see now that I used Calibre's custom column feature and Kobo Touch. Now I'm wondering if that's where the issue is: it might be because the Metadata Management option is set to automatic, rather than "on send" or manual.
Alternatively, it could be because of what you suggested: although I never connect my devices to wifi and I don't allow my devices to sync to Kobo anymore, when I setup my device, it started to sync automatically. Although I disconnected from wifi immediately, maybe it was enough time to create the collections before it downloaded any of the books on my Kobo account (I only sideload, but Kobo loves to add its books over and over
)
I'll try again. I have now deleted all the empty collections (I did that before I posted here). I'll link up to Calibre and if they reappear again (with wifi off), then it's probably something in Calibre but if not, then it was probably the aborted Kobo sync.