Since this was such a hot topic earlier in the day, IDW Editor Bobby Curnow replied with a bit of clarification on how exactly the worlds between the comics and the show actually worked. The basic idea is this:
- The Comics follow the show as closely as possible
- They try avoid breaking any of the show "canons"
- If major elements in a comic idea would clash with a future idea from the show, Hasbro might axe it.
- Bobby is unaware of the show staffers following the comics in any official way
- With all of this, what happens in the comics technically has no bearing on the actual show
So in the end, the comic will follow show canon, but the show doesn't technically follow comic canon.
Editorial bit:
As Jim pointed out though in a series of tweets (starting here), does it even matter in the end? More pony is more pony. I'm not complaining. I don't think the show or the comics have ever been 100% on cannon since season two as is. Ponyland is flexible. It's a playground of civilizations and sapient creatures all appearing and disappearing when needed with "some" connections throughout.
The Analysis community may have pointed a critical eye at the show in the past year and a half, but lets be realistic here, a lot of what they come up with is just speculation for the sake of making entertaining videos. My Little Pony isn't as deep or set in stone as other major settings, which makes a good amount of critical analysis pointless outside of just being fun to theorize with.
So watch your ponies, but don't expect serious business anywhere near what our buddies in the Youtuber pony community come up with. At the end of the day, Twilight Sparkle can mind control an entire city or level a mountain. You can't expect stability with power like that floating around!