Hello Qazi,
Your requirement look like very specific,
As you know all about the Back flush indicator type and functionality, don't waste time on this.
as per standard SAP you have to manually set the back flush indicator in any of option as per business requirement.
Please take help of BADI: WORKORDER_GOODSMVT as Caetano suggested in above post and with help of the Technical team you can achieve your requirement
Regards
Umesh Mali