Hi Denny,
I'm guessing that after your wife updated to iOS 9 on your iPhone, she was asked if she would like to update Notes to use the new features and she said "Yes"
What happened then is that, because the format of the old notes and the new ones is different, Apple split off her old notes and kept them for access on pre-iOS 9 devices and made a new Notes storage for her iOS 9 "super"-notes.
To get them back on her iPhone, you need to open Notes on a Mac running (pre-El Capitan) OS X and open the Notes app there.
Using that, move all her old notes into a non-iCloud account, like Gmail or whatever, and then, when you add the Gmail account to her iPhone (if it isn't already added), then she'll have access to them again.
Post back if you have any trouble with it,
Max.