Anyone ever go back at retcon part of their fic because of changes in the show?

I have.

2509095
I am lucky (and astonished) to say I have not.

My flagship story, Last, which I totally did not invent this group to promote, was inspired by Ex-Nihilos' Rorschach in Equestria, which intrigued me as it is essentially a side-story to Season One. There are a few minor divergences from canon, but nothing serious.
Similarly, LAST is a side-story to seasons one and two. I started it about halfway through Season 3, and I was scared to death that the Season 3 finale was going to mess it all up, but I found that I had hit the nail on the head: My story followed the themes of the show, and the rest fell into place. It was very satisfying.

2513061

Heh, cool.

The addition of the (Season 4 spoiler) Harmony Tree kinda messed something up for me if keeping my fic with canon was something I wanted to do.

Though, it was an easy fix and I think I can use it for later.

2513077
Good for you!
A lot of writers say, "The AU Tag is your friend", and are afraid of restricting themselves to the show's continuity. I found that your story can remain flexible if you keep the restriction, and it allows you to give your own interpretation of the show and it's themes.