Especially when it comes to something like Equestria Girls where it's already established that paradox duplicates can meet.

Do you have a way of distinguishing them? The problem is much the same as having two characters with the same first name, despite the fact in real life that is hardly a rare occurrence.

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I’d say that going the way of using various “names” for the characters is probably the easiest. That means, pony-turned-human is Twilight, her human counterpart is commonly called Sci-Twi. But it also depends on the context, so definitely not the best thing to do every time you refer to the character.

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Have the characters discuss and agree on nicknames early on, and stick to them. 'Twily' 'Flutters' 'RD'. Whatever works.

If this isn't an option, then do your best to make it clear who's who from the context of the surrounding scene.

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Personally, in one of my stories to distinguish both Twilights, I explained that they had agreed beforehand that human Twilight would be 'Sparkle' and Princess Twilight would be just 'Twilight' when together to avoid confusions.
Plus their personalities are different, so the reader is able to tell who is who even if they are not in the same scene together and Sparkle is referred as Twilight by other characters.
If it's a Twilight case or something similar, I would personally not recommend you to use 'Sci-Twi' since its mostly a name invented by Hasbro for the doll to be easy to distinguish from the other one, and it doesn't really have that much context when put in stories.
Try to think about that too, if it's a commonly used nickname for a character but doesn't fit your context, then it wouldn't make much sense. (And I think I'm starting to overthink this lol)

At the end of the day, I think is more about how you play with the resources you have more than anything else.
Sometimes also adding some clarification of who's talking such as the typical 'the ex-unicorn' is useful too.

"Hey, wait a minute," said Twilight Sparkle. She pointed across the school laboratory at where Pinkie Pie was inflating balloons with the water faucet. "You can't be here. I saw you go into the portal to go visit your alternate dimensional duplicate on a trip out to the rock farm."

"I did?" Pinkie Pie blinked several times, then popped like a balloon in a shower of confetti, leaving the rest of the class to stare in horror.

Well, all except AppleJack, who continued to get out beakers for the science lesson. "Dagnabit, Twi. Couldn't you have waited until after class?"

i used to have a girl friend with the same first name as mine -- Terry vs Terri. And we had the same middle name. We used to joke about the confusion if we ever got married.