Context: TCB happens and Humanity is forced off of Earth, after reaching another planet we rebuild our civilization. But due to a variety of disasters we kind of had to start over from scratch, so no perfect digital records. You know the lost colony trope.

How would future humanity try to explain or rationalize the very bizzare series of events that transpired on Earth? For instance maybe the commonly accepted theory was that it was some mutating virus that emerged due to climate change and ravaged Earth. Many may find the idea of actual magic horses invading Earth to be too implausible, kinda like creationism.

A disease that decimated the Human population or a final war that had Biological warfare used that made the series of events play out. I do agree the "Magic horses invaded" would not be thought of until they manage to return to Earth or something.

7586256
Earth was invaded and they were driven out. It doesn't take a whole lot of thought to simplify what happened. There's no need to make up crap about a virus or whatever. Maybe exact details would be lost, but an alien invasion that kicks you off your homeworld isn't something easily forgotten. Heck I doubt the survivors would LET it be forgotten. Nah, they'd make sure it was remembered what the enemy looked like, and that any future alien contacts are to be looked upon with suspicion. And further disasters and suffering would just reinforce it, since Earth would probably be looked back on with heavy nostalgia goggles compared to wherever they ended up, so they'd just blame ponies more for every setback.

Tl;Dr, humanity wouldn't forget about the ponies. They'd hard bake demonization of ponies into their culture.

It would most likely be written about the same way we write about World War II.

7586368
I was thinking of rifters when I came up with that idea
7586394
In that case then I'd see a lot of demonization and exaggeration. I'd imagine that by the current day historians would try to sift through the first person sources to figure out what actually happened

7586564
In which case they'd turn up nothing about a virus and a whole boatload of reasons justifying humanity's current xenophobia.