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Your question seems totally unrelated to KOReader.
Also calibre, on its default config, its pretty hardcoded to each device stock settings.
There's a chance calibre won't figure out the books are already on device until those books are not recognized/scanned by nickel.
I'm not a heavy calibre user, so my suggestion might sound weird to fans out there:
1. disable kobo driver and whatever kobo plugins you have.
2. use connect to folder. Push books that way.
3. setup your wireless inbox to the same dir used in 2
With these 3 steps you'll be able to push books wired and wireless. It should behave ok mixing both methods and you won't rely on whatever stock thingies calibre expects there.
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