I created program and added 4-5 workflows in the program management interface. I could remove the workflows from the interface (clicking the [X]) and they would disappear.
When i go to the patient dashboard, search for a patient, then go to the overview tab and try to add a new program, on the window that pops up, i still see the deleted workflows under the "Initial States (Optional)" section. They should not appear here since i deleted them.
You could look into ../WEB-INF/view/portlets/patientPrograms.jsp and/or org.openmrs.web.controller.PatientProgramsPortletController