Hi @sierra_adare-ta ...
I just tested this in my own sandbox course. I created a brand new, empty course shell. Then, I used the Course Import Tool to import content from my existing sandbox course (which had three weighted assignment groups) into the empty course shell. Once the course import completed, I looked at my "Assignments" page in the new course, and everything looked identical to my original sandbox course. All assignments from the original course stayed in their respective assignment groups. None of them moved unexpectedly to the "Imported Assignments" group. Maybe this would be something you should report to Canvas Support to see what they have to say?