You can create a new RRD graph report in an existing properties file or in a new customized graph properties file. You can run in trouble if you have more than one report definition with the same name, e.g. two reports with the name "netsnmp.disk". One of the graph gets overwritten and your changes have no effect.
If you delete a graph report, you have to restart OpenNMS or - if you have splitted setup - the webapplication to get rid of the report definitions in memory.