Student Work for a Lesson / Module that is subsequently Unpublished will still be retained by Lt - however it will not be accessible by either Administrators or Students until the Lesson or Module is Published again.
If you want to allow Students to still have access to their work, you should switch the Grading Mode to PDF Grading (Course of Interest | Settings | Grading Workflow) and prompt the Students to log in and download any PDFs they wish to retain, prior to Unpublishing.