I just downloaded Calibre and would like to use it for my Kindle books. I have two questions:

I understand I can download all the books I have on my Kindle at once by connecting my Kindle to my PC. Does it take the books off my Kindle so there is nothing left on it, or does it copy the books to Calibre? I would hate to have to copy them again if something went wrong.

After I do whatever I want to change in Calibre, will it put the books back in my collection folders on Kindle, or will it just dump the books without putting them into the original folders?

Thanks for the help. I'm a little intimidated

I understand I can download all the books I have on my Kindle at once by connecting my Kindle to my PC. Does it take the books off my Kindle so there is nothing left on it, or does it copy the books to Calibre?

It just copies it to Calibre. To delete the book you have to actually select it and chose "delete".

After I do whatever I want to change in Calibre, will it put the books back in my collection folders on Kindle, or will it just dump the books without putting them into the original folders?

I have a Paperwhite. If you just copy them back and forth, they won't go into collections on mine. You have to re-file them on the Paperwhite.

Now, there is a Kindle Collection plug-in for Calibre, and the forum for it is HERE. You might want to read the entries on what the program does at the beginning, then go to the latest posts to see what it does now. (It was released in 2011, so I'm not up on what upgrades they've made to the program.) I didn't have the right kindle for it to work, and just haven't been back to see if it works with the Paperwhite. There's also some other programs around that say they work with Kindle Collections, but I haven't tried them out or looked into it very much. 

Thanks, Cindy, I'll give it a try and check out the Collections thingy.