Comment 1 for bug 2006726

This is something apple broke in safari, you should report it to them.
It is not replicable in chrome or firefox (and on ipad all browsers are
actually safari thanks to apple, no matter what their "skin" might be).

You can work around it by simply quitting and restarting safari, the
bookmarks will then show up. It's only on reload in safari that they get
lost. So avoid doing reloads or if you must then quit and restart.