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I use Calibre for that. There is a plugin for 'Kindle Collections' as well. I just did something similar a few weeks ago.
1. Calibre; and get the Plugin for Kindle Collections.
2. In Calibre, make up a new custom column (preferences, add your own column), to store the names of your Collections when you use the Kindle Collection plugin.
3. after plugging in your kindle, copy your books from your kindle into calibre (yeah, might take a while if you have a lot).
4. Use Kindle Collection plugin to copy the collection tags from the Kindle to the books that are now in Calibre.
5. Do whatever cleanup you need on the Kindle itself (If you really mean to wipe it, just go to the drive letter\Documents, and delete everything in that folder)
6. Back in Calibre, copy all the books back to your now-empty Kindle.
7. I cleaned up my collections in Calibre first; put things in only 1 Collection for example. Then I used the plugin to put the collection tags onto the books on the Kindle.
and, done!
Note that some things will be lost, I think, if you wipe it like this. Some of your metadata, like highlights or notes which are stored in the Kindle:\Documents\MyClippings.txt, or bookmarks in bookname.MBP or bookname.apnx file. But I'm not really sure about that. If you're paranoid, before wiping out Kindle:\documents folder, you may want to copy the whole thing to a backup location locally on your computer, just in case you have something important in those files.
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