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Pretty much. Your best bet is to use Authenticator Plus (https://play.google.com/store/apps/details?id=com.mufri.authenticatorplus) or something like that, backs up to local files or Dropbox (p/w protected) and syncs across devices. That's what I did when I set up keepass to generate the TOTP codes for me.
If you select 'can't scan' then it will give you a code - note it down and you can use it to add it to authenticator apps after the fact, like you're wanting to do now. That code is all the QR code actually contains, it's the seed for the time-based code generator.
hamrack
I've just bought a new phone to replace my HTC one as the battery has just about given up. I use google authenticator for a few sites. It looks like I need to disable 2 step on all sites I use it on and then re-enable with my new phone. IS this correct? Seems a bit of a ball ache.