@DanielBarwick ...

Unfortunately, you'll first need to remove the rubric from all but one assignment in your course.  That is why you are seeing the message "Rubrics cannot be modified once they have been used in more than one place."  I know this might be a pain (I've had to do it myself when I built courses for instructors), but this is the only solution I'm aware of.  After you remove the rubric from all but one assignment, you'll be able to edit the rubric as needed.  Then, you'll need to re-add the rubric back to the assignments.  Now, I'm not exactly sure what happens if you've already used that rubric for assignment grading (i.e. you've already scored student assignments with that rubric).  Other folks here in the Community might be able to shed more light on that.

Sorry I don't have a better solution for you, but I hope this helps in some way.