If students still have the file shared with them but it is no longer in their course folder because it has been moved). There are a few things you need to consider.
If the student is the owner of the file they will continue to have access to the file no matter where you move it. If you shared a file where you are the owner but they can edit or view, once moved from their course folder students will no longer have access (providing the new location is not shared with students).
For files that the student is not the owner of this support article can give you more information,
If the copy file was used in Hapara, students are the owners of the files copied to them. Students need to remove themselves as owners and give you ownership when the assessment is finished.