So, depending on Sal's definition of 'about 15 years', it's possible Vito left Empire Bay in late 1951 or early 1952 (16 years and change based on that scene, which takes place in February of 1968) while it could've been later (1953-54) before he left town. In the meeting in Mafia III where Sal offers Lincoln a job, he talks about Vito being sent down by the commission 'about 15 years ago'. It's entirely plausible and quite likely that any bad blood between Vito and his sister was still in effect at this time. In the five chapters after 'A Friend of Ours', Francesca isn't referenced again. The final mission of the game takes place on September 26th, so two months have passed since the confrontation.

At this point, it's made very clear that Francesca doesn't want anything to do with Vito because he beat the shit out of Eric and makes it clear that he'll do it again if he has to. In Mafia II, we see Vito's confrontation with Francesca's husband Eric Reilly on July 27th in the Chapter 'A Friend of Ours'. IIRC, Lincoln asks Vito if he still has family out in Empire Bay, when Lincoln first visits him for his side missions of avenging Joe.

Mafia 2 vito