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At this point in the semester the regular add/drops have slowed down, but we start to see a sharp spike in new 'courses' being created in myCourses because of the honors designation.
For all the details on what happens as part of the honors designation process you can read this description provided by the honors program: http://www.unh.edu/honors-program/designating-course-honors
The important thing to note is in the second to last paragraph, "the Registrar will create a special Honors section of the course, and transfer the student into it". When this happens the student is also removed from your general course in myCourses and put into a new, honors specific course. Most faculty members want the student to remain in the regular course to participate in class discussions, access materials, receive announcements, etc....
To accomplish this you want to cross-list the honors section with the original course. This article explains how you will go to the honors course and cross-list it, so the student and all their information will be back to the original course: https://unh.edu/it/kb/article/mycourses-cross-list-combine-course.html
If you want to manage the honors specific assignments and grading in myCourses there is a tool called differentiated assignments which lets you create assignments specific only to a specific course section (Honors section) or student. Read more about that feature here: https://community.canvaslms.com/docs/DOC-2630