I assume you are referring to the namespace prefix declarations on top of Turtle files? They are just a representation of whatever prefixes are in the underlying graph. If you delete them from the graph, they will be gone from the file too.
But I am unclear about which tool you are using and how you are exporting. In Composer you can delete prefixes from the "Home" resource of the ontology, and in EDG they are managed on the Settings tab.
Holger
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