This is a refactoring point; it changes everything in your project in accordance with your new changes. If you do not want the files to be dynamically updated at a repeated ratio, I suggest you remove them from your project. This allows you to continue to use the reuse function without dropping files that you do not want to modify.
EDIT: Also, you can check this out , it is on Google books and talks a bit about netbeans re-factoring.
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