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Updating from Reader to Acrobat should not have deleted anything from your device. This was just another update that changed the name and icon, and added some new features for Acrobat DC Pro subscribers. Everything else for our Reader users should have remained the same.
I have a couple of questions:
Were you logged in to Acrobat.com, and were your files stored on Acrobat.com? If so, you may need to ensure that you log in to Document Cloud (the new name for Acrobat.com) to see the files.
Did you delete Reader from your device before installing the new Acrobat app? If so, unfortunately when you delete an app iOS deletes all of the local storage that app uses. For iOS to keep your files around, you need to just let iOS Update, rather than our users deleting and installing fresh. If this is what happened, I'm sorry, but I don't know how to retrieve your files.
[discussion moved to the new Reader/Acrobat DC for mobile forum]