Especially in this show, the memories of having something happen does not mean it happened. All the main characters have multiple versions of memories of their pasts in their heads. Versions of living in Storybrooke, versions of raising Henry, wish world versions, rewritten author versions. That doesn’t mean that all of those things really tangibly happened. That is the problem here.
It is a problem of their own making too. They were very clear when they created the wish realm. That it wasn’t real. It was a created construct of Emma/split Regina’s wish. Real Regina did not murder a Snow and Charming and then steal a version of Henry’s mother leaving that Henry parentless and desperate and alone. They wanted to make sure that we knew that it wasn’t real because of that.
Then they lost most of the cast because they didn’t want to be on the show, so they just decided to ignore what actually happened on the show. Regina pretty much created a situation where there is now a Henry who could become darker and more evil then she was as the Evil Queen and they have just completely ignored that, so that they could take that Hook and reuse him while keeping real Hook with Emma in Storybrooke.
That is the entire game here. Now, they are pretending that fake Hook is a real person who has existed for hundreds of years and that actually did these things. They just took something that existed and rewrote it, just like they have done many times before, just like they rewrote the characters of Regina and Hook many times, just like they rewrote Emma’s backstory, and Regina’s backstory, and Snow’s, to the point where the show is just one big convoluted mess that doesn’t make any sense. That’s it. That’s the show.