What does updating delete folders on iphone?

Why is it that every time I plug in for an update, the update deletes all my file folders? I stopped using them rather than recreating them with every update. Thanks!

It shouldn't be that way.  Before the update, a backup is made.  After the update the backup is installed and all your apps, folders, settings, etc should be as they were prior to the update.
Try reinstalling iTunes.

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