Locking position of layer when source file changes?

Often times when working in After Effects, if I change something as minor as the stroke width in my Illustrator source file, the position of that object then shifts when updated in After Effects. Then, if that object happens to have children, their position changes too. I understand that if i'm changing the shape of my original object, by nature it's going alter it's placement but when changing something as minor as the stroke a half point size, I then have to spend x amount of minutes fixing the placement everything, it seems kind of silly. Any suggestions on a work-around for this?