Has any movie taking place over long periods ever re-shot scenes with an actor when they are older?

François Truffaut directed Jean-Pierre Léaud as “Antoine Doinel” in a series of films that went through stages in his life from young boy to young man to a married man. It’s not one film per se, but it is the same character playing a young person and an older person. I suppose the same could be said of any movie with sequels, but this one really shows the age difference - the timespan is decades. The Before Trilogy also has this kind of timespan, except it doesn’t show “Jesse” as a kid. Damn, that would’ve been cool to see a movie that does the same thing with that character using the same actor (I like to imagine he’s the same character from Dead Poets’ Society).

In Layer Cake there's a flashback scene where a gangster reminisces about an earlier time (early 70s) when they were committing crimes and living in debauchery they used the much older characters playing their younger selves. It's kinda hilarious because all they did was give the actors cheap looking wigs but their aged and wrinkled faces didn't create the effect that they were "younger" in the scene.

There's another movie called "Sunshine" with Ralph Fiennes who plays several generations of Jewish-Hungarian men from the same family from the late 19th Century to the Communist era in Hungary. In some scenes they insert Ralph as the younger version of each generation, but then as the story moved forward they'd age Ralph with makeup.

"I am wondering if a completed and released film has ever gone back and replaced the scenes with the same actor, just older. "

No, I've never heard of such a thing. Quite a hassle to bring back the same actors and exactly recreate the scene so it fits into the movie.