To update a menu, select the link above, click "settings" and change the file it links to. Do that for each menu you want to update. Publish all pages. Go to the site and click on "menus". Click on the button you just made. Copy the address.
Go to Pages on the left. Click the settings icon (the gear) for each menu you've updated. Select the URL that page directs to, and paste over with the new URL that you've copied.
Go to Pages on the left and select the gear (settings) for "menus". Select Menu Dropdown (formerly called "Toggle Submenu Only"). Publish all pages.
It's not your imagination. This is clunky as shit.