I'm a bit late but FWIW Google Authenticator has a QR code export option, it generates a giant QR code (potentially multiple) that contain all the accounts and

I'm a bit late but FWIW Google Authenticator has a QR code export option, it generates a giant QR code (potentially multiple) that contain all the accounts and secrets. It's designed for you to scan into Google Authenticator on another device, but you can also read the contents of that QR code yourself with various open source utilities to get the accounts and secrets (or just print a copy for a physical backup of them). Overall it's not a terrible way to go, though like you said if you can save the original QR codes that's a nicer way to do it.