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Did you use Calibre's "Send to device" option to copy the ebooks to your Fire? If so, the ebooks should be automatically detected when you disconnect in Calibre and then hit the Disconnect button on your Fire. They will likely show up if you don't do the disconects, but this is the safest approach.
The PDOC stuff is a red herring. Check both the Books and Docs apps and any Calibre-produced MOBI should be in one or the other.
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