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You may need to force your Kobo to do a full rescan of books to import the new ones in its own DB (if I remember correctly, Koreader does not modify in any way Kobo own sqlite file)
If you have already NickelMenu installed, you can add a line in the config file
menu_item : main : Rescan Full : nickel_misc : rescan_books_full
to add the option on NickelMenu
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