I have the same problem and I'm the developer stuck trying to figure out what to do.
Not only is MY menu gone, but a new horizontal menu is present with ALL pages listed - which wraps my entire page.
It also moved my RHS bar ads, to the very bottom left of the page.
And, my footer links no longer work.
This was an automatic WP update that hosed 4 of my main money sites.
Can't find a way to manually create a horizontal menu in the new wigdets... and for sidebars, the options are Before content and after - not 'beside" content... so, i can't find a way to get my pages looking anything close to before.
It's quite a mess and the templates came from several different places - all impacted.