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If you mean the collections were there but were empty it’s because they get synced to your account.
I don’t think anything would wipe them out short of making a new account which of course doesn’t really wipe them out it just doesn’t associate them with the new account from the old.
As to why, probably because Kobo figured most people doing resets would rather not have to recreate the collections which is more work than deleting them. YMMV of course but I’d expect Kobo to aim at pleasing the masses.
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