Hey @MK_COLBURN!

Great questions and thanks for exploring the Community for answers!

Think of the items in modules as short cut icons to the actual location where the items are stored.   For example, If Assignment Z shows in Module 1, that is not the "real" Assignment Z.  It is just an icon with a link to the assignment that is housed in the Assignments area of your course.  That is why the options menu to the right of Assignment Z in the module gives you the option to Remove and not to delete the item.  You can remove it from the module, but that assignment is not deleted from the course.  

Now to address your concerns...

Unpublishing one or more modules would not cause any loss or work submitted, grades already in the grade book, or the ability to grade late work that has already been submitted prior to unpublishing the modules.  Everything still remains in the course.  Upublishing the module(s) would only mean that students would no longer be able to see that module or access any of the items that are still housed in the unpublished module.  Therefore, if students still need to submit work, they would no longer be able to do so, unless either the module would be published again or the assignment would be removed from that module and was still published.  You would just need to make sure that students knew where to access the assignment for late submissions (such as a different published module or using the Assignments/Quizzes/Discussions link from the course Navigation menu.

Hope this information helps and some stress has been alleviated.  Please respond if you have additional questions.

Good luck!