To replace regular QR codes in IRN-generated documents with signed QR codes, go to 
Business Settings > Accounting  Options > GST Config > Enable Signed QR codes for IRN-generated documents:


Additional Resources:

How to Generate E-invoices through Refrens? (India) 
How to generate E-invoices for SEZ and Export? (India) 
How to pass payment details to E-invoices? (India) 
How to generate E-invoices for Credit and Debit Notes? (India)
How to Create GSP User Name and Password to Generate E-Invoices on Refrens? (India) 
How to show IRN in a single line in documents? (India) 
How to view e-invoice acknowledgment no. & date? (India) 
How to fetch & update E-invoice status of the invoices generated/canceled outside of Refrens? (India)

How to cancel an E-invoice? (India)