You can delete your novel, individual chapters from the novel or individual submissions from each chapter.
What this does is it disconnects each contained submission from the novel, but you never actually delete the submission itself from the novel page.
Here is an example:
I have a novel with three chapters, each one with two submissions (part 1 and part 2).
I have rewritten part 2 of chapter 3 and decide to switch the old submission out for the new one, so that people reading the novel will get the newest version.
I click the 'x' next to the submission in the novel detail page.
The old submission is now 'disconnected' from the novel. It still has the same name as it did before, but if you go into the submission you will see that it has none of the novel features and is no longer present on the novel page.
I now rename this old submission to something like My novel name ch 3 (old draft) and submit my new draft into a Queue of my choosing.
When I submit the story I select the novel and the chapter as the place I want to submit to. The submission now becomes Part 2 of the Chapter 3.
You can delete whole chapters or even the entire novel in the same way. This will disconnect all the submissions so they'll become just regular submissions without any of the bells and whistles of the novel system. You can disconnect and reconnect submissions from your novel at will.
Please note: Deleting stories is not the same as deleting submissions in a novel. If you delete your story (so that all its text is gone) it is not disconnected from the novel.