I experienced a similar problem. I imported assignments from course 1 to course 2, which were all copied into an "Imported Assignments" group under assignments. I deleted this group. When I imported assignments again from course 1 to course 2 and added them to modules in course 2, they would show up in the module but I could not see them in assignments. It appeared that deleting "Imported Assignments" messed up with Canvas's file system.
I solved the problem by going to modules where the assignments showed up, clicking on the assignment, and then editing the title (eg. just adding "--" to the end) and saving it. Then the assignment with the edited name showed up under assignments, at the top most group.
I hope this helps you as well.
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