I keep thinking that each time they've messed with Control (or have tried to stop it), they've moved closer to the original timeline/series. So things are changing gradually, little by little. Didn't their communicators change to the ones we see in the original series a few episodes back? So maybe the time crystal thing-y re-sets things to the way they are meant to be? Maybe the re-set means that things aren't quite as advanced as they are in the current Discovery time-line.
Any time travel thing in any tv show/movie/book gives me headaches (we will not discuss the time travel in Stargate SG-1 that screwed up my brain)! Mostly I just have to go along for the ride and just pretend I have some idea of what's going on or accept what the writers want to play with.
