Answered on September 18,2019
As you have got Non-utilization certificate from Pune RTO, you have to cancel the NOC. You can now cancel the NOC by submitting the non-utilisation certificate in the Maharashtra RTO along with an original copy of NOC, RC, Insurance. So, NOC issued from Maharashtra RTO will be canceled.
When you cancel the NOC, it means that your vehicle belongs to Maharashtra.
As you are plying your vehicle in Maharashtra, but at a different RTO jurisdiction, it is not necessary to re-register your vehicle.