your bookmark should not be deleted when you upgrade.
any how you can also backup your bookmarks
your documents bookmarks are part of the qvw files so there isn't a problem with them you can always bring a copy of the model
your server bookmark are saved for each model in a sharefile which you can backup
and replace the file if it been deleted during upgrade
i just perform an upgrade from QV12 to Qv 12.1 all bookmarks are intact