I think I have figured it out. Reinserting same figures will disconnect old site and effectively make them "phantom". So all you need to do is to check the site area.
;;originated from
;;
http://www.theswamp.org/index.php?topic=42585.msg477730#msg477730;;by BlackBox
(defun c:AeccDeleteParcels ( / #ACAD# #ACADDOC# aeccDoc ss)
(defun Civil-version ( / )
(rtos(atof(vl-registry-read(strcat "HKEY_LOCAL_MACHINE\\"(vlax-user-product-key)) "Release"))2 1)
)
(defun Exitprompt ( msg / )(alert msg)(exit))
(setq #ACAD# (vlax-get-acad-object))
(setq #ACADDOC# (vla-get-activedocument #ACAD#))
(setq ss(ssget "x" '((0 . "AECC_PARCEL"))))
(if (not(setq aeccApp (vla-getInterfaceObject #ACAD# (strcat "AeccXUiLand.AeccApplication." (Civil-version)))))
(exitprompt "Could not connect to AeccXUiLand.AeccApplication.")
)
(setq aeccDoc (vlax-get aeccApp 'ActiveDocument))
(setq oSites (vlax-get aeccDoc 'sites))
(vlax-for x (vla-get-activeselectionset #ACADDOC#)
(if(=(vlax-get(vlax-get(vlax-get x 'Parcels)'Statistics)'Area)0)
(vl-catch-all-apply 'vlax-invoke (list oSites 'remove x))
)
)
)