@blus ...
Unfortunately, there isn't a way that I know of to tell Canvas to combine two or more assignments into just one assignment. Further, you cannot manually move assignment submissions from one assignment to another. You may need to tell your students exactly which assignment they should be submitting their work to...even if it means they have to re-submit to the correct one. Then, for the duplicate assignment, you could set it to not count towards the final grade.
Also, you might be happy to know that in a couple weeks, instructors will be able to submit assignments on behalf of students. So, if something like what you describe happens again, this might be another tool for you to use to ensure all the assignments are being submitted to the right space in your course. You can read more about this at: Canvas Release Notes (2023-03-18) - Instructure Community (canvaslms.com).
I hope this will help a bit. Sing out if you have any other questions about this...thanks!
