Quote:
Originally Posted by lsi
I'm confused now. 
When I buy a book from Amazon, it lands in the documents folder on the Kindle. I usually then copy it to the Calibre library on the PC as a backup and to organize the collections. If Calibre then sends it to the documents/calibre folder, I suppose I will end up with 2 copies on the Kindle: one original in documents and another one in documents/calibre?
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True, unless you then delete the copy from your original purchase and keep the copy managed by calibre. I never considered it an issue because the first thing I do when I purchase a book from Amazon, Barnes & Noble, or (as of a few weeks ago) Apple is to strip out the DRM so that everything in my calibre library is DRM-free.
I'll have a think on it and see if I can come up with a solution that does not require #4 but still allows one to have collections and content not managed by calibre live in peace with that managed by calibre.