That happened to me often. Changing to 'store all items', suggested by LessThanYouThink I believe, and the Kobo iPad app update in late March fixed it.
I have just under 50 books and I had created 2 new shelves, Unread and Read, which I found useful. I haven't made any extra shelves since the changes for fear of upsetting what's working. Has anyone got shelves in the iPad app and found it stays stable?
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