At some point, Wordpress merged post & link categories and changed up some of the functions. It was awhile ago and I don't remember if it was before or after the old version you're upgrading from.
I don't think it affected stock default theme layouts, but if you were using the functions to display links a certain way, that would go screwy.
If I remember correctly, I had one site where I called the links by category in different parts of the page. After the upgrade, those sections just listed all links and made it a mess, so I had to update the function usage in the theme.
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