I’m interested in stories where a character was retconned to be an impostor who replaced the real character long ago.

Alicia Masters was replaced by the Skrull Lyja is Fantastic Four #265 (1984), but this was only revealed in Fantastic Four #357 (1991).

Bobbi Morse was replaced by the Skrull H'rpra in Avengers: West Coast #91 (1993), but this was only revealed in Secret Invasion #8 (2008).

Aunt May was replaced by an impostor in Amazing Spider-Man #392 (1994), but this was only revealed in Spectacular Spider-Man #262 (1998).

Black Bolt was replaced by a Skrull immediately after the Silent War #6 (2007), and this was revealed soon afterward in New Avengers: Illuminati #5 (2008).

Elektra was replaced by the Skrull Pagon sometime before New Avengers #29 (2007), and this was revealed soon afterward when she was killed in New Avengers #31 (2007).

Jessica Drew was replaced by the Skrull Veranke sometime before New Avengers #1 (2005), but this was only revealed in New Avengers #40 (2008).

Proty's soul took over Garth Ranzz's body in Adventure Comics #312 (1963), but this was only revealed in Legion of Super-Heroes Annual #3 (1992). Since the Crisis on Infinite Earths happened in between these two stories, I don't know if this retcon applies to the pre-Crisis continuity. I also don't know if it applies to the post-Infinite Crisis Legion continuity which is similar to the original continuity but not quite the same.

In Star Trek: Deep Space Nine, Julian Bashir was replaced by a changeling sometime before the episode sometime before the episode Rapture (1996) and this was revealed soon afterward in the episode In Purgatory's Shadow (1997).

Can anyone think of any other examples?

Maybe young justice Roy?

Pretty sure that was done once in Simpsons. Nobody liked that episode.

Hank Pym was replaced by a Skrull and was revealed around Secret Invasion. The Skrull had a kid with Tigra.

Not sure if this counts, but a delusional Hank Pym from when he first became Yellowjacket captured and betrayed a composite Avengers team in Avengers Forever. There were two Hank Pyms in the story from two different times (story was around 1998). Around 2000 - 2001, Hank split into multiple Hanks in the Avengers series, with one Hank kidnapping the other and replacing him on the team. The multiple Pym story line was resolved in Avengers Annual 2001.

It's always the bloody Skrulls.

She-Hulk who slept with Juggernaut turned out to be her counterpart from alternate reality.

#NotAllSkrulls

@netspiker: Secret Invasion came out in 2008 I believe.

@solid_snake97: That was typo. Thanks.

Long ago or long time in the future who went back to the past... Then I suggest Ivar Timewalker

Not sure of exact issue numbers, but a loooong running arc, that ran through several other titles was the life model decoy of Nick Fury.. A story they have adapted in the AoS TV series.

Also, I believe Ultron secretly assumed the identity as Jarvis a while before his big reveal?

Oh, and how can we forget, the Red Hood unmasking as the Joker?

I'm gonna have nightmares of the Clone Saga again. Thank comics that they retconed that retcon.

Lol, is that legit?

Also classic Swamp Thing, he was not a real person but found out he was a construct made by the Green.

Of course don't forget a modern example of Harrison Wells in the Flash TV show.

Edit again. Battle Star Galactica revolved around this.

I would actually check TV tropes, this is surely a trope.

so true

Hey didn't the Skrulls take the form of Mr Fantastic, the Thing, the Torch, and some cows in Avengers 93 during the Kree/Skrull war too? It's always the Skrulls.

I don't think all of those were actually retcons. Some of them were likely planned out the way they were beforehand. The biggest one that never fully happened was supposed to be Superman in the 90's. It was supposed to come out that the original Superman had actually died years prior and been buried under the sand(which would tie into some earlier story) and that the current Superman was some sort of doppleganger. It didn't happen because dc felt like it would be too similar to what Marvel was doing with Spiderman at the time with his Clone Wars saga.