I'm on a team creating a top-down jet shooter. I need to create a different colored exaust trail for each kind of jet. I use the Fire1 particle system and adjust it. Then in the hopes that it won't affect the Fire1 itself, I put it into an empty Object, a new prefab, AND put it into a jet. Yet if I make any changes to the color, it still affects the Fire1 default system anyway.
Are you adjusting the prefab or the material? If it is using a shared material, changes to the material will affect everything that uses the material. In order to resolve this, you will need to duplicate the material and set you duplicate prefab to use this duplicate material.
.. or you can create generic prefab with default material and apply different material to an instanced GameObject