Just saw this, loved it, I think people who talk about timeline or paradoxes are reading the non linearity idea wrong.
Time is seen as non-linear, but it isn't fixed, the loop can change, it's why the aliens arrive, if it was deterministic there would be no reason for them to came to earth, you can't change the present by going to the past because the reason you are in the past is what happened in the present, basically the paradox from the Time Machine, but that isn't the case here, there is no time travel at all, is about perception. Aliens are more advanced, so they can either perceive or at least make predictions about bigger loops, that's where the 3000 years thing comes from. Louise can only perceive her own life, probably only the part about Ian and Hannah as a loop, she can't perceive beyond that, but she definitely can change the loop, that's why Ian said she made the "wrong choice", there is choice in the non linear perception of time.