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As you figured out, EpubMerge does not have such an option right now.
I could add such an option, but if it's a common problem with Kobo, I wonder if there isn't an existing solution? Or if there should be a general tool for it instead of an EpubMerge option? Or an enhancement to Calibre's Edit TOC tool?
(Do you really use EpubMerge from CLI? I didn't know anyone did that...)
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