Hello Sir,
As i understood from your query that now you have two separate GST Registrations and here is my reply to your query in regard to both the registrations:
For old GST Registration: Now as your GST number has been reinstated from July 2017 then you can surrender the number from the back date and in case commissioner inquired you about the reason for surrendering the number from back date in that case you represent the whole case to him. If he agree to your concern than he can cancel your registration from back date without any interest and penalty. But in case he won't agree to your concerns then he may ask you file all the returns with interest and penalty. Now you have to decide either you want to pay the interest and penalty now or take a chance to save it.
For New Registration: File regular returns in regard to new GST number and in case there is some pending amount that has to be paid at the time of old GST registration then you can also pay that by filing the FORM -DRC-03 on the GST Portal.
Thanks and Regards
Divya Chugh