The reason for the behavior you observed is that Blend re-uses its resources. To avoid the problem you are having, you need to rename the default brushes used in the template. You need to do that only for the first copy of the default template - when you first edit a copy of the default template, rename the default brushes, and then when you edit a second copy of the default template, Blend will create yet another copy of the default brushes (with their original names). this way when you edit one of your custom templates, the other will not be affected. I am attaching a screenshot that shows how to edit the brush names. Let me know if you need further assisstance.
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