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You can put MOBI ebooks into either the Books or the Documents folder. In either case, it is the cdetype record inside the ebook that controls which app (Books or Docs) "owns" it. If this is EBOK (Calibre's default) they will show up in Books, and if cdetype is missing or set to PDOC (Calibre's alternative option) it will show up in Docs.
Calibre always puts the ebooks into Documents, but it is the cdetype that matters.
If you email the ebook to Amazon, they automatically add PDOC before sending it back to your Fire.
Note that you can't use sub-folders for ebooks, they all have to be in Books or Documents (e.g. not Books\Author_Name or whatever).
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