You only need to resize the prefab once, and all other instances will be of the same size.
1. Plant the prefab in your scene, preferably near a human height object for scale comparison.
2. Open the prefab in the inspector - click on the object inside your ASSET folder, NOT its copy in your hierarchy.
3. Find the handy "Resize" setting right at the top. Alter it until you are happy with the size.
4. Confirm before exiting the Inspector. Done.
If you have other instances of that prefab already planted in your terrain, they probably will shrink to a very small size, because you already resized them and altering their prefab adds a second level of miniaturisation to them. So you best remove them altogether before doing this.