Hi Santosh,
Just stumbled upon this post of yours. I hope you might have already got a solution for this issue. It is really an interesting scenario.
I think this should be a standard SAP behaviour. Creation of Purchase requisition by way of deleting a PO is as good as manual creation of PReq in ECC. This PReq will be seen as PPDS PReq in APO.
Please share what solution you applied to get this back as SNP PReq?
Regards,
Ravi