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As this module is working well with CCK Node reference so it should provide the facility to work with Hierarchical select Node reference module
By making following change, it will work with Hierarchical select Node reference field
file : popups_reference.module
line no : 113
if ($widget_type == 'nodereference_select' || $widget_type == 'nodereference_buttons' || $widget_type == 'nodereference_hs') {
Thanks