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Well if they are imported into Calibre, Calibre should be able to find them. If you have no imported them into Calibre, that may be your problem. You need to set Calibre to look for books in subdirectories (click the little arrow next to add books). Also, in addition to the issue of zip files (everything must be unzipped first), if you have any that are really .doc format, they will not work. Finally, I found after having done something similar myself that sometimes the files you download are simply not formated correctly and Calibre can't read them. Try opening the file in the ebook reader. If Calibre can't open it in the ebook reader, you have a corrupted file.
I'm sure others with much better knowledge will be along with additional suggestions, but these were just based on my experiences downloading various books and importing them. I ended up trashing a bunch that were just not importing correctly.
Eric
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