Okay. I'll try to answer these in orders.
There is no need to ever unpublish a chapter in order to edit. Just hit the edit button.
This is by design in case an author unpublishes a middle chapter. We had far too many support requests of "I'm reading Story X and it goes from Chapter 9 to Chapter 11. What happened to Chapter 10?" In the off chance someone unpublished a chapter, all following chapters are automatically unpublished.
This is currently a bug. It slipped by in the previous mess and I've alerted the programmer.
I put a support request into the forums software folks and this is their reply:
This bug was fixed and appears to be broken again. The work around is to go to Advanced Search https://www.gayauthors.org/stories/browse/sort/
Select: complete, Sci-Fi and set Word Count to More Than 1000 (or any other number) and it will work. I've reported the bug to the programmer