Advance reversal - rcm if dedcuted twice

Last year in Septemeber 2017, we deposited RCM charges as part of the advance received from a customer for supply of goods. 

2 months later we raised a supply invoice to the same customer & delivered the goods. A month later, we mentioned this sale in GST 3B and deposited full GST (and didn't reduce the GST deposited earlier on advance). Now last month during our audit we found our mistake. So, my question is can we just reverse the entry in GSTR-1 and take the credit of that amount or do I need to apply for a refund?

Thanks

Nitin