Uhhh .... errr ...
"Moral of the story is somebody should be telling people with the 2.2 version of Assignment's to remove it before the upgrade to Moodle 3.6."
A little history concerning assignments in Moodle ...
mod_assignment shows as 'Assignment (2.2)' in the GUI. It is the original Assignment module.
Around version 2.3 of moodle, a new assignment mod named mod_assign made an appearance.
In the Site Admin menu, there was an 'Upgrade Assignments' link that when executed converted all mod_assignment modules to mod_assign. Once all Assignments were converted it was recommended to hide (still is the recommendation) the old assignment 2.2 so Teachers/Course Creators wouldn't use the old mod.
mod_assignment is still present in git acquired code for 3.6.x and below.
It is hidden by default in the Site Admin menus for plugins and I believe is present in case Site Admins/Teachers are trying to restore old course backups (2.3 and below) that used the old mod_assignment. If unhidden, site admin can convert those old mod_assignments to the new mod_assign easily. And after conversion, once again hide 'Assignment (2.2)' in the Admin GUI.
So am not certain that the advice about removing a core mod is the right thing to do - depending upon factors of course.
Not at all sure the troubles you had weren't self-inflicted - happens sometimes - don't think anyone will ever really know.
'spirit of sharing', Ken