So my sister got mad at me and took my ds and snapped it in half so she had to get me a new one, and it has a different 3ds friend code, will that reset progress towards a new train station? :/
It shouldn't I don't think. I wanna say it's measured in game. You can sit on your tree and check. At the very end of the credits it will tell you how many visits you have.
Well, that was a colossally stupid thing for her to do! And the expense of replacing it? Wow!!! Anyway, I'm glad you got a new one. I think the above posters are correct. The data is saved on the game itself. Your FC will change, of course, but I don't think that affects anything else in the game at all.
Dare I hope she had to get you a skin you liked, too?
I think you'll be fine if you have a cartridge game. As for digital, I have no clue. Regardless, I think you'll be fine, plus you have a brand new 3DS, so your situation isn't so bad.