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Install the KoboUtilities, create a column to stored the collections read from your Kobo, connect your Kobo and run Get Shelves From Device from the Kobo Utilities menu. I recommend a separate column from the ones you are using to create collections from calibre's tags/genres/whatever. That way you can look at them and decide which ones you want to use.
At one time I had close to 60 collections based on various criteria plus ones based on series but ended up removing most of them as improvements in Kobo's firmware made them unneeded. The only one that currently survives is the #finished column.
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