Could Pepper Potts have saved Tony when he snapped at the end of Avengers: Endgame due to her regeneration powers from Iron Man 3 or do the Infinity Stones somehow override her regeneration powers?
No, she couldn’t have.
It’s briefly stared at the end of the Iron Man 3 movie, that Tony removes the Extremis from Pepper’s system.
And even if that removal was unsuccessful- there’s not any evidence in the MCU that I’m aware of, which suggests Extremis regeneration is transferable like that and capable of healing anyone but whose system it’s pumped into.
Pepper would only be able to heal Pepper.