Books purchased from Kobo will be in the .kobo/kepub directory. The file name is not obvious, but, it is shown in the device list in calibre when you click on the book. The file name does not have an extension, so you need to add this before adding to calibre. Use either epub or kepub.
But, if the book has DRM, this will not work. The DRM needs to be removed before it can be used elsewhere. The Obok plugin, which part of the DRM removal tools, can do this. It can also be used with books without DRM.
Alternatively, you can download the epub version of the book from the Kobo store. You will still need to handle DRM if the book as it.
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