Where are you transferring the books to? Kobo stores its book in a specific folder but you can't use that directory since it is not scanned for new books.
I would suggest creating a directory in the root of the exposed partition, eBooks for example and then configuring your save to device template in the KoboTouch (or KoboTouchExtended if you are using it) driver.
My current template is:
Ebooks/{author_sort:sublist(0,1,&)}/{title} - {authors:sublist(0,1,&)}
Basically, store the books in a directory derived from the first author sort entry with the filename as title - first author in the author list. This just keeps the filename and paths shorter.
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