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After restart, go to Site Admin → Ingest Data → Manage Jena Models.  Review the named graphs.  You should see:

Removing Removing the myOntology.owl file from the filegraph directory and restarting Tomcat will automatically remove the named graph.  This will remove all ontology assertions made in myOntology.owl.  It will It will not remove any abox assertions using myOntology.owl from the content triple store.