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OK, I've made some progress. In Calibre I looked at the metadata of one book. In the Custom Metadata tab I changed the name of the My Shelves field to the new category name (so I typed it in as it was as yet an unexisting category). Lo and behold, the new name is added to the list in My Shelves in the right sidebar.
However, this new collection is not added to my Kobo when synced. I've looked at the Kobo plugin in Device Interface Plugin and Create Collections is ticked, so that should work, shouldn't it?
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