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No, the phones are OK.
What freaked me out was installing the desktop client and seeing 8 accounts. Uninstalling and installing on a different desktop and seeing 6 accounts. Did this a few times, different number of accounts each time but a few similarities in that it was some of the oldest accounts I could see.
It's weird... if they encrypted my whole account and delivered it to me as a single file that is decrypted locally I'd expect to always see every account.
But that's not what happened, it looks like an API call to Authy that the desktop client makes which is then returning a non-complete set of accounts.
I don't think the mobile clients use this... so they're OK. But as I have so many accounts I now want peace of mind and to know I've got the master secrets in more than just Authy.
I installed Authy on another phone as a backup if I killed mine. Do I need to be concerned?
I've never noticed account differences but I don't use PC Authy, only phone.