From Calibre, go to the Kindle device (along the top icons) click once on any book, ctrl+a and then hit del. That should remove everything from your Kindle without destroying the basic file system on the device. Then you can select all the books in your Calibre library and "Send to Device". Once thats done, disconnect Kindle and wait for it to resynch everything. It'll automatically synch any and all books bought through Amazon, as well as the user guide junk and dictionaries etc from your Amazon account.
I had so many issues using Calibre with my KT at first, but I've mostly solved it by converting all my ebooks to .mobi and manually deleting all other formats from the individual metadata edit. As I add new books to my library it's pretty simple to convert to mobi and edit the metadata as I go.
Edited to add - From the Kindle section in Calibre, you can copy all the amazon content to your Calibre library for ease of organisation. You can also use the "On Device" sort column to see which files are ticked as being already on the Kindle, so you can select and "Send to Device" for the ones with no tick. Makes it so much easier to keep track of everything
