By Following this Process I was able to submit the form without the Prefill not showing error
1. After coming to the last page of submission in the Agile Pro-S Form, the DIN/PAN is not prefilled, so simply click on the submit button It would show the error that the DIN/PAN is not mentioned. (Its all right).
2. Click on "My Application" and go to the Mini Dashboard Section of your Incorporation Forms.
3. You would see that next to the Agile Pro-S Form, Submitted will be written.
4. Edit the Agile Pro-S form again and fill all the details, if missing.
5. You will see the DIN/PAN Prefilled.
The above mentioned juggad worked for me, twice. I might not work for you, but you can give it a try.