Will resizing assets inside c2 harm it?

If I resize assets after I bring them into c2 will it mess with the game at all?

It shouldn't but keep in mind the size of the animation in the animation editor is not the size it will appear in the game and that is determined by the size you set in the layout UNLESS you are creating an object in which case it will be the size you set in the animation editor.

For that reason if you will be creating objects set them to the size you want them to appear when created.