|Yeah, I know it's spelled 'Flurry Heart'. I bet 'Fluffy Heart' would have sold more toys... but not McFlurries.|
So let's start by noting the two obvious differences these two have: the huge fucking wings and the eye color. Eye color is easy enough: In humans it's generally well known that a baby born with light blue eyes can change color drastically while they're growing up. But is it the same with horses? Actually, yes, they can change just as frequently according to this forum full of actual horse owners. So Flurry Heart having light blue eyes and Starlight Glimmer having purple eyes isn't a problem.
Then there's the wings. Buckle up kiddos, because this is where the conspiracy theory goes from dull to batshit insane! So remember awhile back when Pinkie Pie had to babysit a pegasus baby and a unicorn baby, and their powers were crazy strong at the time? Something about babies being temporarily able to use their powers to their full ability before growing up?
|You know, this one|
You might be thinking, "Fuck you, that's too OP!", but remember: With each new alicorn princess this show churns out the newer ones overpower the older ones. Celestia having her ass kicked by Chrysalis, only to be saved by Cadence. Then Cadence not only needed Twilight's help for the Crystal Empire in the season 3 opening, but gave her magical power (along with the other two princess's) to Twilight in order to defeat Tirek. And shit, in season 5 the show already proved that Starlight Glimmer can outwit Twilight easily with her time travel abilities.
So let's keep building on this theory and assume that Flurry Heart has incredibly destructive alicorn abilties as a baby that can't be controlled by any of the other Princesses. If they can't control her, how do they stop her? Simple: They take away her powers, even if they think it's only temporary. Now, if you were a parent in this situation, what would you do: Take away the wings, the horn, or both?
Taking away both would make raising the baby much easier, but then they would lose essential years of learning with those body parts. So then it's between the wings and the horn, and if we're going on the assumption that this is past Starlight we'd take away the wings. It does make sense though: unicorn magic not only takes years of practice, but intense schooling up to university level to conquer. Twilight learns how to fly in like, what, 1-2 years? They could wait until she's 18 and more responsible to give her back her wings and she'd be fine.
So now we've got a debuffed Flurry Heart baby that is missing its huge ass wings. How do we get from there to Starlight Glimmer? I'm thinking that as the months go by of Flurry's first year in the world mom and dad get to wondering how to raise their kid. If she's raised in a castle, told that she's a perfect princess by everyone she knows and has servants left and right to do every single chore for her is she going to turn out a spoiled brat? Would she be able to handle her (eventually unlocked) alicorn powers responsibly? Remember that even though Twilight Sparkle and Shining Armor moved on up in the world they had relatively normal childhoods. If the books are to be believed as canon then Cadence also had somewhat of a humble childhood.
They decide to get a normal looking house in a super generic looking town and pretend to be a normal family, never telling Flurry about her heritage. They change their appearances with wigs and dye, lie about their jobs and change their names to blend in. (I guess Cadence would hide her wings under clothing at home and then go to work everyday naked? I dunno, you fill in the blanks.) Needless to say any alicorn visitors would also need to have a disguise on when visiting the household. And when the time came to pick out Flurry's alternate name, Cadence would remember Twilight's super powerful unicorn friend. Gee, she sure does look a lot like Flurry, and she's recently changed for the better. Maybe I'll name my kid after her... AND THAT'S HOW THE TIME LOOP HAPPENS KIDDOS, NOW GO TO BED.