I still have not managed to find out the issue with windows. For now, only mac and linux work correctly. Help would be greatly appreciated with the windows issue. It seems that the container.xml in the zip somehow is not being stored correctly. This may be a golang bug.
Now for some good news: I have added series metadata updating support to kepubify. It currently only works on linux, but windows support is on the way. The command will get the series metadata from each book and update it in the kobo. I have tested it with firmware 4.6.9995 and 3.19.5761.
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