Making this all a future which will eventually be undone is a terrible, horrible, no good, very bad idea.
I mean, you already have a situation where Discovery's adventures over the first two seasons - although they happened - are more or less swept under the rug by Section 31 as "it's classified." If they basically undid whatever they're doing in the 32nd century as well, then in a certain sense the show itself has no legacy within the timeline whatsoever. It also shows that the writers have no idea how to actually build on the world they are creating, and just repeatedly wipe the slate clean and try again with something else.
I still have a strong suspicion though that the show is "on the bubble" in terms of renewal though. I'm not yet predicting that this is the last season, but Kurtzman was pretty final about them never returning to the 23rd century, and we now know production of the Section 31 show is set to begin basically as soon as this season is over. I could see them at minimum putting Discovery on a longer hiatus to allow for space to air Lower Decks and Section 31.