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How does it get the books into the database? Is it updating the database or triggering the book processing? Or waiting for the next time you disconnect to a PC?
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The preferred launcher, for KOReader, (KSM8) provides, to Nickel, a "fmon" icon named "simulate_usb_connection.png". Using that you can trigger the book processing, or you could connect to your PC yourself.
For the rest; there is no technical reason to believe both using the same file would actually cause a problem, so I may be a little paranoid, in that regard. I do though prefer to avoid the Nickel processing when transferring a number of books that may include some not meeting Kobo's high standards, but that read well enough in KOReader and/or Coolreader.
Luck;
Ken