I have a prefab, which is way to small at scale 1, so I changed it to 25 but that doesn’t seem to apply on a treeinstance, and changing the height/widthscale on the treeinstace only changes the size of the billboard:
If your instance has been changed in anyway then it becomes an individual instance and will not update automatically when the prefab is changed. You need to click revert at the top of the inspector to make it a true copy of the prefab again.
Also if you created you prefab from this object then although it may have gone a blue color in the hierarchy window it may not be a true instance, I always delete the original and place a definite prefab instance in its place once created to be totally sure.
You are best changing the scale in the 3D model import settings. Keeping your Unity scale uniform at (1, 1, 1). This can make a lot of things much easier later on 