Personally, I think it makes a lot of sense to use the auto-add and have calibre delete the already-added books.
How else does calibre keep track of which files have already been auto-added?
You can set your Amazon account to automatically queue new books for Kindle for PC/Mac. Launch Kindle for PC/Mac and new books will be auto-downloaded. Launch calibre and they will be auto-imported.
This works fine unless you actually think Kindle for PC/Mac is a useful reader application instead of just being a tool to easily download your purchases. In that case, I cannot help you...
...
Of course, if Amazon would fix their software to not use retardedly obfuscated filenames (or reveal a public API allowing calibre to interface with your Amazon account
), this problem wouldn't exist.
But there is very little chance of that happening, and there is nothing calibre can do about it.