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Welcome to Kobo-world. No, It won't cause problems. Kepub is the proprietary Kobo version of epub. Both work on your Kobo. The kepub enables several features that are not available if you use epub. Have you installed the Kobo Utilities plugin on Calibre? It is a very helpful plugin. There are plenty of threads in this forum to help you get the most use out of your Kobo.
Enjoy your Clara. They are nice little ereaders.
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