Good Day Rish,
the underdelivery tolerance can be max 99,9%, not more. So for zero qty delivery system is still waiting for another delivery and does not tick the delivery completed indicator. You can create a new outbound delivery anytime.
As far as I know there is not standard possibility to update PO line item from inside the EWM.
I think this is the custom logic, so BAPI_PO_CHANGE can be used for this. Normally the PO document remains open and is relevant for next VL10B job. You can use mass change MEMASSPO tool to update lock field or delivery completed indicator field to prevent PO item getting into the next VL10B.
Regards,
Petr