late fees and penalty under gst

Sir,I have business,I take new GSTN in 27 th september 2017,on regular basis by mistake, but we filed all 3B and Return in the month of july 2017 (after nine month from DoR) upto November 2017 we show some transaction and than filled nil return and paid late fees around Rupees 40000 and applied for cancelation of that GSTN but now govt.comes with notification said that july 17 to upto sept 18 they waive all late fees. So my question is can we get refund that amt? And how. And what procedure to get that 40000 rs. Please guide us....