Indexes can be deleted. When deleting, the entire contents of the index will be removed as well as its associated configuration. A new index can be created with the same name at a later point in time.

IndexManager index = graphDb.index();
Index<Node> actors = index.forNodes( "actors" );
actors.delete();

Note that the actual deletion of the index is made during the commit of the surrounding transaction. Calls made to such an index instance after delete() has been called are invalid inside that transaction as well as outside (if the transaction is successful), but will become valid again if the transaction is rolled back.