To avoid this issue, make sure you've logged into all your 2factor accounts, and have the new Authenticator QR code ready -before- updating.<p>eg. For Google accounts: 'Move to a Different Phone' at <a href="https://accounts.google.com/b/0/SmsAuthSettings" rel="nofollow">https://accounts.google.com/b/0/SmsAuthSettings</a>
IIRC this happened with an update to Google Authenticator for Android as well. They rolled out a new version that discarded all your old accounts, and removed the old version from the store. Quite a nasty surprise...
I believe this is related to iOS 7: <a href="https://news.ycombinator.com/item?id=6112077" rel="nofollow">https://news.ycombinator.com/item?id=6112077</a>
Other discussion: <a href="https://news.ycombinator.com/item?id=6325760" rel="nofollow">https://news.ycombinator.com/item?id=6325760</a>