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Originally Posted by ownedbycats
No quotation marks.
I think the Kobo wifi sync thing ran at some point between the two connections. Could that have restored the collection?
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Kobo syncs the collections and which purchased books are in the collections. It does not sync anything about the sideloaded books. If you sign out of the device and back in, the collections will all be created, but, they will have no sideloaded books in them.
If the driver deletes a collection, it does it in a way that should mean it will be deleted on the server when you sync. You could probably come up with an order of syncing and connecting to calibre that will confuse things. And if there is a second device involved, it gets a bit more confusing. I don't have the delete empty collections selected as I don't have the same books on all my devices. That was causing collections to disappear when I connected a device with only a few books and then synced it and the others.
The handling of this isn't perfect as there are two distinct systems involved and they don't necessarily work by the same rules.