Yes, if you change the gallery files it will affect all who are using it. The workaround is to copy the gallery folder, name it something else unique, and edit the <title> in the [new gallery]/admin/design.xml file. Then your admin will show a new selectable gallery in the admin choose gallery section. You can now edit your new copy and apply it to your home page gallery without affecting the other galleries you already have set up.
-justin