If you've created a myTeamSpeak account, make sure that you're logged in and that synchonization is enabled in Tools -> Options -> myTeamSpeak. If you weren't or had synchronization disabled then you should most likely have your items back afterwards.
If you never created in account when the client updated and launched:
Did you try starting the client multiple times? Or again because you thought it hadn't started?
In any case, you can get your stuff back, check %AppData%\TS3Client or InstallPath\config for a file called settings.db.pre-sync_ followed by a date.
You should find one of those in there as well as a ts3clientui_qt.secrets.conf.bak.
Make a copy and rename them to settings.db and ts3clientui_qt.secrets.conf respectively and start the client. Your identities and bookmarks should be back now.
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