Nick reported that Crew Manager Modify Settings "Save All Changes" causes the Automatically generated site menu to disappear on the e33 epiphany site at 4:05pm on Friday 5 April 2019.
I was able to duplicate the problem in the WordPress Admin panel for those with Skipper privileges. This has been corrected and all Crew Manager sites have the fix as of 5:00pm Friday 5 April 2019.