Need a little help trying to find a story, I read a story a couple of years ago where Pinkie Pie turns out to have been a pegasus and her parents were ashamed of that fact and apparently at one point decided to cut her wings off. can't remember much else aside from that it's just something that popped into my head I remember that section in the story but I cannot remember anything else. Any help to locate this story would be appreciated, thanks.

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I'm pretty sure it's not the one you're looking for, but one of my first stories was The End of Innocence in which Pinkie gets magical wings so she can be with Thunderlane, as Zecora's rebels try to hold out against Queen Chrysalis, but the magic starts to fail.
Sorry I'm not familiar with any other stories using this idea.

Pinkie is not the main character of the story so it might be a little harder to locate.
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You might try Inkbunny: they have a comic based on what you've described; of course, the site is semi-NSFW so please be careful...