Since you're using Calibre, you could easily use the Kindle Collection Manager plugin to do this. Read the collections off your current Kindle into Calibre, download the files to your new Kindle, and then create the collections from Calibre.
NOTE: if you haven't removed DRM from your books on the Kindle, then you can't just copy the files from one Kindle to another. Even though they are on the same account, they are DRM locked to the individual device. You will need to re-download them from Amazon. Of course, if your normal workflow has removed the DRM, then you can copy them.
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