Hi Srinath,
When the delivery completed indicator is checked, the PO item should be removed from MD04 and RRP3. If the order is not getting removed at APO side, then try to find the reason...Check if the material and plant are included in the imodels: materials and purchse orders.
If after running CCR you still see the PO in APO, check the queues in ECC and APO using SMQ1/2. Check also if you have an entry in the CIF post-processing CPP. In both places you should be able to see the error log explaining the cause of the problem.
Finally, try to delete the PO using /SAPAPO/RLCDEL.
Kind regards,
Mariano