Hi Shyam,
Whenever the PR line items are flagged for deletion, it still gets copied to the corresponding PO.
If system messages are maintained for this as either W or E, the system will issue either a warning or error message before saving the PO.
If the system message is not maintained, please make sure it is maintained so that it will alert the creator of the deleted line items in PR.
Alternative solution:
If you want only the non-deleted line item in the PO, please drill down in the document overview till the line item level and drag only the items which you want to be in the PO.