The controls that are added to the master page cannot be edited in page edit mode. The controls that have been dropped to a master page should be edited only from the template. If the control is declared into the masterpage directly or inside the code behind you cannot edit it through Sitefinity. Controls base scripts and stylesheets should be disabled only in case that you have scripts/stylesheets that will ensure that the control will keep working properly. You can gather more information at Disabling embedded resources
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