So was Twilight confused back in the season 5 opener, or are there two Meadowbrooks

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It's entirely plausible that Twilight was simply misinformed. Historians have brought to light all sorts of details about individuals, and it might've been that History Marched On between the start of Season Five and now.

As for how that misconception started, well, there may have been a lot of uppity tribist unicorns quietly convinced that any well-known magic user couldn't be some simple Earth pony.

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If I might present an alternative, the 'Meadowbrook' Twilight talked about, was known that way due to an error in translation, the translator simply translated everything literally. Or the name is like Confucius, the philosopher, his real name was Kong Fu Tzu (Master Kong)

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That works too.