Glad you have it sorted, but sounds like your IT department needs to coordinate with you about upgrading things for your moodle sites. :|
Noted your screen shot showed 'classic' theme to be upgraded .. there are only 2 themes that come with core ... boost and classic. Best to leave those directories. Matter of fact, many force the theme to boost via config.php file just prior to upgrades to avoid issues with 3rd party themes not being compatible with core upgrade.
And this is your test site ... so what about your production site? Did this experience give you the plan for your production site upgrade?
Kinda curious as to why either boost or classic was missing since those are core themes.
And one more comment ... if site was installed/maintained by git repo (command line only) this issue might have been avoided - or resolved more quickly and with less confusion.
'SoS', Ken
by Ken Task.