While the timeline doesn't necessarily invalidate post-X6 events, it does raise an eyebrow at the Nightmare being associated with Zero's research stasis. That's a heck of a bomb to drop, as X6 was very ambiguous and did not give any indication as to whether the sealing was related to the rest of the in-game events. To reconcile this with the full X-series, it means the topic of the Nightmare needs to get dug up again. Not terribly difficult, given how X8 references X5, but still, it'd be interesting to see how that happens.
I also find it fascinating that they've placed such a link, the Nightmare leading to Sigma Virus research leading to Cyber-Elves, considering the many correlations between the Nightmare and Cyber-Elves. The large scale control of Reploids by a single master, the manipulation of reality, the stable existence of a program object in the substance world free of any host, and the resulting vulnerability to substance world weaponry. These are all things that the Nightmare and Cyber-Elves share.
Anyway, X7-XCM doesn't really impact the Zero-series, short of Orbital Elevators. The definite bigger impact is on ZX, so what Zan said earlier seems to apply.
Firstly, taking these concepts at face value, Command Mission seems to be pushed to its own timeline unless that story itself was part of the Elf Wars. Zero's 50 year first sealing, the Elf Wars, as well as all of the X series incidents are now reported to fit into a 100 year period (all 1XX years ago). The only other option would be X1's back story taking place in circa 2155, and Command Mission being one of Zero's late adventures before his first sealing.
Is there any reason Cain cannot be using a computer program with 41 year old copyrights (which for some reason have not been renewed)? Because XCM could easily be early 22XX, with the Force Metal meteor having been identified in 2202.
The main issue as I see it is trying to reconcile the 1XX dates with Inticreate's self-expanded series gap. Due to Elf Wars, approximate timeframe from Zero's research-stasis to Zero-series is not 100 years but 150 years. Which means everything from Zero's birth to that point, including the entirety of the X-series, needs to be crammed into a less than 50 year window. While the year 2200 falls between XCM and the rest of the series, the actual time gap has not been stated. Nor has Inti, while telling us that everything we know is wrong, chosen to re-adopt the label of "22XX" for the Zero-series, which they otherwise would have been well reasonable in doing, in light of the timeframe estimates they've given. XCM may be the reason for that.
Placing the "200 year marker" between the birth of X and the birth of Zero was a really odd move, IMHO. Whether we're trying to account for X7-XCM (necessary for ZX Advent) or not, it really does seem to indicate that Wily-ghost was still building Zero very near the X-series. Otherwise, the birth of X and the birth of Zero should not be separated to such a degree.
Do they have to rewrite history every time we get one of these things? I mean, is it that hard to reveal new things without altering old ones? I feel like I'm getting too old for this.
I feel for you. This is getting ridiculous, and is the textbook example of why I wish Inticreates was relegated to the post-Zero-series era rather than commanding the MegaMan saga as a whole. It was popular fanon that the continuing X-series was the reason for the X-to-Zero series gap rewrite, but we know from MMZOCW that was not the case, it was in fact for Dark Elf. In other words, Inti rewrote their own backstory. Here, they did it again, extending as far back as the Classic series. And to what end? This isn't even a new game, it's a compilation. Granted, we don't know how much of this is them and how much is Inafune, but I just get this impression that Inti cannot stand by what has already been established.