I don't know what I did but I lost the highlighting option in iBooks. I don't have the aA on the top right corner anymore. I always keep my iPad up to date and I have not used my iBooks in a few months. Can iBooks be reset to default?
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I just checked on my iPad, which is on iOS 9.1 and it's missing for me as well. If this is a result of an update of the iBooks app, there's no way to get the old version back since it's one of the stock apps built into iOS.