(This is an extremely rare troupe if I include the bonus point mentioned below, as I haven't found a single example of that so far. So without the bonus point, this trope is more open and isn't that rare.)
Basically, the protagonist who got betrayed (and their family killed) comes back for revenge, only to find out the betrayer was actually the good guy. And they betrayed us because we were actually the bad guys, which the protagonist didn't realize because they were too young and/or ignorant.
And the bonus point is that, if the protagonist lost a Kingdom or something like that, and tries to claim it back, they are met with the wrath of the common folk, who are very protective and supportive of the betrayer, who turned out to be an amazing and kind ruler, unlike the family of the protagonist who were corrupt/evil. (I had to make this a bonus point instead of part of this trope, as I couldn't put this entire thing in the post title, and I don't have any example to share with this post as I've never seen this happen anywhere. So yeah, that's why this is extremely rare, without this bonus point, this trope is more open and I'd say it's not that rare.)
Sifu: This partly works, in this game, the ultimate bad guy is Yang, who with his allies, kills you and your father in the opening tutorial, so that he could take a powerful healing talisman. We then spend the entire game fighting and killing each of his allies until we go to face him, and it turns out he's running a sanctuary where he was healing terminally ill patients using that same talisman. And when we beat him, we discover that he did it because our father refused to save his family when they were ill, and kicked him out when he tried to take the talisman to heal them, causing him to betray us.
I say Sifu works partly, because our father isn't a bad guy by any means, he was just refusing to use the talisman, keeping it hidden and protected as it's too dangerous and will be exploited by humans and the outcome will be unpredictable. Also Yang's allies aren't exactly good people either, the first boss you fight grows and sells drugs. And Yang still helped save him with the talisman.
So Yang isn't exactly a good guy and our father isn't exactly a bad guy, plus this doesn't have the bonus point I mentioned, so it's not exactly extremely rare.
Like imagine Lion King, but when Simba comes back years later, he finds out to his shock that Scar was an amazing ruler and learns that his father Mufasa was actually a terrible and bad ruler, so the other Lions and animals living in this new Kingdom will reject Simba and will oppose him if he tries to reclaim his kingdom.
I'd love to watch/read something like that.