Im so sorryvdjdjf so with baby words: history repeats itself but the characters have free will so the results are always different. One time Eren didnt commit genocide, and this time he did. Next time we dont know, but what Mikasa knows is that she is going to see him again which is why it was less harder for her to kill him (because she saw a souvenir of one of her past lives). After their death, life will start again because their life is a loop, but the results will be different because of their free will. Like idk if you believe in resurrection? Many ppl do, they believe they will be reborn again, well thats the case for aot's characters!! idk if that made sense !!

So the time loop theory was the right answer? When the rumbling first activated Mikasa thought back when Eren asked her "what am i to you" and she told herself that maybe had she given another answer (than saying "im family") the actual present would be different. And it was actually true because in another life she chose another answer and they ran away together. Basically snk's world is a time loop, a continous circle but with different paths caused by different choices (like its a loop but the characters' choices arent)hence the reason why she said "see you Eren" when she literally just cut his head.
Also at the veryyy first chapter when they're still kids, Mikasa wakes Eren up and his first words are "huh? Mikasa?when did you grew your hair?" so its really a loop byeee im crying.
And her headaches arent because she is an Ackerman, they're caused by deja vu!!!when she gets souvenirs from another timeline/world it hurts her, but this chapter was the only deja vu where she saw one of her past lives clearly :(( im so empty it hurts