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Were you ever able to figure out a way to resolve this? I have the same problem: a series from the Kobo store had some volumes in a "separate" series because the publisher entered a different name. I was able to associate them with entries in Calibre and update the series name, but they still show as different series on the Kobo device (presumably because the IDs are different). Using KoboUtilities to "Manage series" doesn't actually appear to do anything beyond the original name change.
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