The Kobo Utilities plugin has a function to fetch the collections from the device and populate a column. But, it is intended more as a way to repopulate the columns in calibre after some sort of mistake or disaster. Using it frequently is probably not a good idea.
Personally I do this in the library. I use several reading lists (via the Reading List plugin) for the current state of the books. This include "ToRead", "Reading" and "Finished". When I move the books between the lists, they change a column to include the state which is then synced back to the device as a collection. Though I don't really use those collections as the device has the state and I can use the filters.
I also use the utilities plugin to fetch the reading status of the books when I connect the device. That sets a column to the percent read and I use that when doing the above steps. It wouldn't be hard to have a column set the collection based on this percentage, but, I find doing it manually is good as I also consider other things such as rating and any final edits for errors in the book.
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