Connecting the device to a USB port, telling it to connect and then disconnecting is the only supported way to have nickel scan for new books. There has been a bit of discussion here about simulating it, and I'm sure someone has been successful. You will need to do a search for it, or wait for someone who has used it to come by.
Also, remember that nickel is looking for files with specific extensions. If your downloaded files don't have these, they will be ignored. And they have to be in the right place, or probably better to say, not in the wrong place. Device looks for new books everywhere except inside directories whose name starts with a dot.
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