Short version: before updating to WP 4.5 and on a day when the only known change was adding a page to a submenu via the navigation menu admin all of the menu links of type Custom Link where we specify a URL suddenly lost their href attributes. Links of type Page still have theirs.
After much experimentation I confirmed that deactivating all plugins did not change this but setting TwentyFifteen as theme corrected it.
Theme authors are no longer available for assistance.
Long version:
So far I have managed to confirm that all of the bad entries have no href attribute on their tag so they don’t know what to link to and that all of the ones having this issue are of the type Custom Link where we have supplied an address.
I have disabled an re-enabled all plugins to no effect on this. I have just now updated to WordPress 4.5 which came out today. That did not fix.
I loaded and saved edits to the menu to see if that would re-set. It did not.
Loaded page with JavaScript turned off to rule out jQuery or other JS stripping off the hrefs after rendering. They were still gone.
Tried editing a local custom link and removing host to see if links starting w http were issue but that did not change anything.
Added a CSS class to one of the custom links via admin and verified it showed up on the enclosing <li> on front end but no help with href on link.
So far only support post I have found re this said they had a corrupted database table that caused it. So I ran a CHECK TABLE on every one of the WP tables and all came back as Ok.
Switching theme to TwentyFifteen has all menu items with correct href attributes. Switch back and issue recurs.
In header.php the menu is drawn via wp_nav_menu(array('menu_class'=>'sf-menu')). I am guessing the sf is for superfish. I removed the class and the menu was drawn unstyled but still lacking hrefs on custom links.
functions.php does not seem to have a replacement for wp_nav_menu()
So where do I go next?