I don't know why they disappeared, but as long as you are syncing to Amazon, they will backup your collections, so you won't lose them in the event of a Factory Reset. You can even import your collections to other Kindles on your account. From the
help page:
Quote:
To import a collection from another Kindle:
Select "Archived Items" from the Kindle Home screen.
Select "Add Other Device Collections" from the Archived Items page.
Select "OK" to confirm.
Note: Importing a collection from another device does not import the books or other items to your Kindle if they aren't downloaded already. However, books already on your Kindle that are associated with a collection will automatically appear under that collection name on your Home screen.
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