@Chris D , I have custom navigation. There are only "What's new" tab with it's link changed to /whats-new/posts/, and some other options moved from different tabs into "What's new" tab.
So, during the update, all menus resetting to it's default states (links and tabs).
I think it's wrong to change any user settings (such as Public navigation settings) during update.
Well, this is why we have asked for more information because we actually don't do this.
My best guess at the moment is that you are editing all of the navigation entries in development mode. Any changes made in development mode would be overwritten (by design) but changes not made in development mode would be maintained.