The Soulnado is unfortunately a perfect deus ex for that. I think it would be shitty since the precedent is that the soulnado fucking destroys anybody caught in it (the soldiers sacrificed, scorpion way back in da, etc) but again, this is comic book writing, they could just as easily make one big middle finger exception for the series' #2 like DC did for Batman.
That said, according to MK9, Scorpion knows Kuai isn't the dude he killed and (at least as of Sub's chapter) doesn't think he's the dude who did his family in. The problem there is MK4 canon basically says all it took was Quan Chi saying "hey, it was that guy, I mean" for Scorpion to decide Sub II was the new killer. So if they come up with some bullshit excuse for how Cyber re-came Human instead of the 'nado excuse, they could fall back on that too.
Or (as it seems from Ed's only real retort on the subject) this is a to date unknown Lin Kuei / Cryomancer who just happened to pick up the mantle. Maybe SZ is just some kind of title and when Kuai went rogue, Sektor's dad appointed a new one or just created a new one to keep people from finding out they got their shit kicked in twice at MK. Quan could very easily have said, nope, that's the guy right there, and Scorpion bought into it just like MK4. And this guy would have no idea (depending on how much the LK told him) as to why this shirai ryu skull ninja keeps calling him a murderer, and just be super tired of being disrespected (this has of course been 25 years later, if we assume all the characters shown are "current" and not some time locked past versions).
