If one made havdalah over wine before praying maariv, and then in maariv he forgot to say chonantanu and has already completed shemoneh esrei, would he have to repeat shemoneh esrei?
The Shulchan Aruch rules (O.C. 294:1) that in general one need not repeat Shemonah Esrei for forgetting Atah Chonantanu. The exception where one does have to repeat it is if he also ate before making havdalah on wine:
ואם טעה ולא הבדיל משלים תפלתו ואינו חוזר מפני שצריך להבדיל על הכוס ואם טעם קודם שהבדיל על הכוס צריך לחזור ולהבדיל בתפלה
Given that if someone made havdalah on wine before praying it is impossible for him to subsequently eat before havdalah, your case would seem to not fall into the exception mentioned in the Shulchan Aruch.