If you are asking specifically about a read-only Navigation List, here is a link to a prior discussion about customizations and security: Dynamics Community Forum Thread Details
If you are referring to entries on the far left Project Navigation Pane, select one of the Navigation Lists. Once it opens click the down-triangle to right of the Navigation List name and select Delete.
If you are referring to entries on the far left Home Navigation Pane, right-click on one of the entries and select Delete.
If you are referring to the tool bar below Microsoft Dynamics GP and above the Project.
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