IDomain#refresh is implemented so that it would not load the list of applications if it wasnt loaded before and it would replace a list of existing applications with a new list of new instances:

public void refresh() throws OpenShiftException {
	final DomainResourceDTO domainResourceDTO =  new GetDomainRequest().execute();
	this.id = domainResourceDTO.getId();
	this.suffix = domainResourceDTO.getSuffix();
	if(this.applications != null) {
		this.applications = loadApplications();
	}
}

we should always load the list of applications and we should update applications that we already have (not replace them with new instances).