At one point in time the author of Essentials was recommending that the Site Admin use a 'stock' theme for the purpose of the upgrade. And then, after the upgrade was success, making Essentials the default theme afterwards. Learned that when attempting to git upgrade a site and it failed - cause, the 'new settings' for Essentials was so massive, one would have to tweak php to very high numbers to get the upgrade to complete. Essentials is massive (understatement) and one almost needs to have a 'degree in Essentials' to run it. :|
IF I were you (I do this now with all sites), I'd allow the use of different themes for categories, then create a 'SA' cat - stands for System Admins - hidden - no one assigned any role in it ... and then a 'SA' course in SA cat where the theme is set to a 'stock' theme ... one that comes with the version you are runnning.
I then bookmark the URL to that course.
In the future, if there is any issue with upgrades that might involve the theme, all I need to do is login via the URL to the SA course. From there, I can get Site Admin menus.
Also use the SA course for testing links ... like one to run cron or other 'test' which one could run.
In that cat I have another course ... hidden - no one assigned - that I use for restoring courses via file system repo - course is minimal and has really nothing in it cept pages/lables to remind System Admins of things.
Oh yeah, the pick list for blocks might only show 'Admin bookmarks' *or* the 'Admin Block' ... which at the course level is related to the Course Admin block. Reason it didn't show for you, it was already there. When that gets dis-associated, one had better be a DB guru to find the associations and context desired to get the admin menus to appear in frapped courses.
Anyhooo ... glad you got things sorted. ;)
'spirit of sharing', Ken