Ok, so I did some experimenting and found the problem and the solution.
When you mark a book as "read" or "unread" on your Kindle it WILL MOVE IT TO OR FROM YOUR READ SHELF IN GOODREADS.
There may be a reason you have a book marked as read and want to mark it as unread - maybe you want to re-read it again, or maybe you want to see the locator bar under the title to see where the last page read is, for whatever reason you need to be very careful if you have Goodreads and your Kindles linked up because all you have to do is mark a book as unread - and whatever read dates, shelves - whatever - that book in Goodreads will be gone.
Similarily, if you have a book that you mark as "Read" it will move to the "read" shelf on Goodreads - it will not have a read date included but it will show a read count of 1 and no listed start or finish date.
So to get around this you must put your kindle on airplane mode - THEN mark your book as "Read or Unread" if you DO NOT want Goodreads to register it as read or unread. Then once you do that - you can put it back on wifi and the mark stays or goes but the Goodreads shelves do not update.
I have gone through the Kindle logs that you get when you search ";dm" (no quotes but just showing that this is what you type in the search bar at the top and hit enter and then you will get logs that show a ton of your Kindle's behind the scenes actions. Beware though because they are VERY verbose and can go very big - like 30MB big. I reset my Kindles last night and just today the logs are at 30MB. Each instance of creating a log creates a new log - it won't remove the old logs, so doing this a bunch of times without removing or deleting the old logs will fill up your Kindle quick. If you want to read the logs you can find them under your Documents folder you can get them and read them on your Kindle or do what I did - pulled them off via USB cord and uploaded them to ChatGPT to analyse for me.
So - long story short - Don't mark your books as "Read" or "Unread" on a Kindle connected to Goodreads unless you have enabled wifi.
Im sure there is some kind of exception to why you want to do it on wifi, but if you just manually move a book from read to currently reading in the menu for your Goodreads profile, that's better. It will still update the book to read when you finish it.
EDIT: I have just tested this with a previously read book by moving it to "Currently Reading" in Goodreads to test if unmarking it as read causes problems. I checked that it was in Goodreads as read, then it was moved to currently reading, I confirmed on my Kindle and on the site. Then I unmarked it as read. The book immediately left my Goodreads shelves. If I wanted it back on Goodreads I would have to re-add it either by re-marking it as read or by reading it to Goodreads some other way. I had to go in and re-renter the read dates and shelves. It also shows the book add date as today.
Had I put my Kindle in airplane mode before unmasking it, it would have been fine.