Her original design had blue instead of red markings (except the markings under her eyes and back legs, because those are scars). It lasted a grand total of 1 day before realising that design wouldn't work for what I wanted to use her for.
She was made for flipnote, and I wanted to colour my animations. You could only use two colours, and in order to make "brown" you had to use both red and black. I couldn't use blue if I did that. Her first image is not on TH because it's framed in my room XD
If I'm being 100% honest, she was never supposed to have black markings at all. Back then, I'd line all of my colours, so it gave the appearance of being a marking. I liked how it looked, so the black boarders got thicker over the years and they became markings.
A bit of a funny story, but i changed her tongue from red to blue after drawing this picture. At the time, I thought it was the funniest thing I've ever made, so I kept it. It's officially canon that her tongue is blue because she painted it, and the colour stayed. Kinda defeated the purpose of not having blue markings, but shhhh that's not the point
After the initial design, I gave her wings because [insert stereotypical "everyone gives their fursonas wings at some point" BS here]. She even got an entire backstory as to where the wings came from, but even back then I thought it was stupid and nonsensical (even in her canon universe), so I scrapped it. Her wings would come back later in her alternate form though.
Her ears have probably changed the most. They started as very long, floppy hound like ears. Her breed wasn't decided until about a year after I made her, so I just picked aspects of dogs that I liked. Back in 2012/2013 I drew my head's really big, and her floppy ears started covering up too much of her body, so I made them half floppy. Then one was up and one was down, then they were both up but people kept calling her a cat or wolf, so I made them floppy again only shorter. I love her floppy ears.
I attempted to change her hairstyle once, but I hated it so I changed it back.
IRL I got glasses in 8th grade, and because Sonie is supposed to be me, she also got glasses. TBH, the only reason she doesn't have them anymore is because I kept forgetting to draw them XD. This seems to be a reoccurring issue with my characters.
A more minor change, but once I learned what saturation was I made her a lot less neon. Yes, she is still pretty brightly coloured, but if you look at her old art vs her new art you can see what I mean.
That's about it honestly. Anything else evolved slowly over time as my art got better