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This is totally normal. The logout from Kobo account deletes the sqlite database and all material download directly from the Kobo Store, whether it was done via a WiFi sync, or Kobo desktop.
You are cautioned before hand that changes since the last sync with Kobo will be lost.
Side loaded material is still on the device and will be readded when the Kobo account is signed back too (or a new and/or dummy account made).
If the collections had been made by calibre the next attachment to calibre will recreate the collections.
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