I went through my Manage Your Kindle page and noticed there were LOTS of books that said that there were updates available for this book. Well I went ahead and updated them all.

A couple questions though:

What are the updates usually? Just cover changes, or fixing errors? Or is there actually changes to the story? (im hoping not, since several of them I have already read. I hate to think about the story line changing after ive read the books!)

The other thing I noticed was that most of them were just replaced on my Kindle with the updated versions. A handful of them though are still in my 'collections' and are also showing up at the end of the collections, as if they are new books downloaded. Why is that? Do I need to go into my collections and delete the former versions and then place the updated versions in my collections?

ETA: Oh and I dont know if it makes a difference or not but mine is a Kindle Keyboard 3G.

There was one I did recently, and the new one replaced the old one, went into the collection but had a "new" badge, as I recall. Most of mine were archived so I did hit "update" anyway.

There are probably different reasons for the update, most likely it's to correct formatting issues, I think.

What are the updates usually? Just cover changes, or fixing errors? Or is there actually changes to the story? (im hoping not, since several of them I have already read. I hate to think about the story line changing after ive read the books!)

Unless the author leaves a note in the book description, or you had both copies to compare, I don't know how you'd tell. It may be mostly formatting, since that seem to be a problem with a lot of books. But it could be for any reason.

I don't know how to re-do them in Collections.

Formatiing is one.  It one update they just removed a few copied chapers.    They dont proof read the ebooks IMO  so when some one complains they fix it.  I think they are just in a rush to get ebooks out they dont care how they look.   

Thanks Ladies!