I think... it will all be clear once you play story mode.

This is purely my guess, so bear with me.

1st timeline: original MK1-MK:A games (not counting the non-canon ones)

2nd timeline: MK9-MKX <-- and MK9 is just ditching the 1st as if it never existed or you can say that they created a second universe (like in DC comics you have alternate realities, it's the same pattern here).

Ok, so first let's make clear that NRS can't get their s**t straight story-wise since MK:DA (well, maybe MK:D), they wanted to start anew with MK9 but it still was a failure. Some ideas were good but as a whole it was a trainwreck.

They never really admitted MK9 is canon and the old games should go to the bin, so we have two separate timelines going side by side and going apart at some point (precisely when Sindel murdered everybody in like... 5 second video... which in the original (1st) timeline is somewhere in the middle of MK3).

Now since they can't think of a pretty good (I'm not even asking for a very good) story, they just recycle the first three games (written mostly by non other than John T. who is no longer a part of NRS).

And knowing that your best bet is to count on the new chick to bring back the heroes from the 1st timeline OR 2nd timeline but before NRS messed it up in MK9 so they can recycle those characters again and butcher the new, horrid ideas they came up with.

It seems like she's bringing fighters from the original (pre-MK9) timeline, like Liu from MK2 and Kung from MK3.

It's irrelevant from which timeline they are when Kung says so, because the future for them (in any case) is insane.

And that is still in the original timeline, however Raiden created another one when he made some of the changes in MK9. So, no Deadly Alliance (because Shang Tsung was killed by Shao Kahn in MK9), no Deception, no Armageddon anymore in this timeline. So, since both Liu and Kung are in this MKX timeline, they know now only about their MKX future, not the DA/D/A one.

The characters Kronika brings back are from the MK9 timeline.

Deadly Alliance was the last well-thought out story. Every bio, ending, and Konquest mode text tied in perfectly together.

Deception was where things started to get messy with numerous retcons, resurrections, and inconsistencies. It's been downhill since.

Man I really wouldn't count on it with the quality of writing we have been receiving for the past two MK games. They usually leave you asking "Why!?" at a higher frequency than you were going in.

story of MK11 will be another messy thing, thats for sure. it will look great, play great and all that, but we will be still confused in many ways.

You're right that the Deadly Alliance is no longer imminent in the new timeline, however I see no proof Armageddon is no more. As a matter of fact, in either Kenshi's or Takeda's endings (maybe both?) in MKX, we do see that Taven is encased in stalegmite, just as he was in the original timeline.

Now these endings are often not canon, but the allusion suggests that nothing has changed that Delia has her vision of Armageddon before MK1, and Argus acts on this, he doesn't act because of Raiden.

Deception is another story, it's unclear how Raiden's timeline shit messed with the potential return of Onaga. In Cassie's MKX ending she kills Shujinko (and kills Deception's story arc by doing so; no Shujinko, no return of Onaga). Again, it's likely a noncanonical ending, but seems to suggest that NRS is disinterested in Deception era material.

Look, all the characters are still there in MKX timeline - Daegon, Taven, Shujinko, Kira, you name it. Some were killed (like Kobra), some still live. But Armageddon as event never happened here, it most probably was delayed, but there was 25 year jump, so if you compare with previous, original timeline - the chain of events is so different now. Hence probably Kronika is so disturbed, apart from imbalance.

This is how I understand it too. The thing is, I don't think there are 2 separate timelines in MK. I mean, there are as far as we, the players can perceive them, but by rewinding time, the way Raiden did in MK9, he didn't just create a new alternate universe or something, as far as we can tell, he had completely overwritten the original timeline, so it's not like in the context of MK9 and MKX, there exists some parallel realm where the original events took place, Raiden had erased all of that. They're still the same characters, and presumably, everything that happened prior to the MK tournament, is still the same, their origins are still the same, but what happens after simply changed, so Liu Kang who defeated Shao Kahn and Shinnok had completely ceased to exist, Smoke who turned into a cyborg had ceased to exist, Onaga ceased to exist, because he was never reborn. Etc. Etc.

So yeah, we'll see what Kronika's exact plan is, but as far as I can tell, she can't just go to the previous timeline to pluck the fighters from it because that timeline doesn't actually exist in the MK universe (or multiverse) as it stands now.

Well, Boon in his interview with Gameinformer said that they tried to play with the concepts of Multiverse. Also multiple characters in their intros say about different timelines.