For a non-delivery of a letter by the post office for your own non availability, it is fault at your own part. However, you may call up the PIO and ask him whether the reply was delivered by Speed / Registered Post or Ordinary Post.
If the delivery was attempted through Speed / Registered Post, then you may request him to provide the tracking number on telephone itself, and then you can track the entire delivery attempt on the internet and verify the reasons for non-delivery.
Also if the delivery is made through Speed / Registered Post, then that a postman makes two attempts for delivering an article, before he returns it back to the consignor.
You can also collect the reply from the RTI office.
Yes with ID proof the person can go and collect it from the post office.
The letter will be kept in the post office for maximum 7 days only, so collect it within 7 days.