Kepubify
From MobileRead
kepubify is ePub to kepub converter created by geek1011.
[edit] Overview
kepubify is a standalone tool to convert ePubs into Kobo ePubs. It does not depend on any other software such as Calibre, and runs on Windows, macOS, and Linux. It is a command line tool, but on windows, it can be used by dragging the ePub file on to kepubify. It has full support for all the main requirements of a kepub, including Kobo Spans.
kepubify also includes a tool to update the series metadata in the Kobo database based on the metadata in the epub files.
[edit] Usage, examples, and FAQ
See the official documentation, as it is updated quite frequently.