When you perform PRE- PROCESSING the program will set Deletion indicator to the PO line items so that it will termed as Archived , so you need to reverse this effect in order to over come the message.
Please use this SAP note it explains how to remove deletion indicator on PO which has been set by PRE PROCESSING program
1905073 - How to reset deletion indicator in Purchasing document header (EKKO-LOEKZ) ?