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If an epub is being displayed with the RMSDK renderer, you can get page numbers at the top and bottom (in book and in chapter) plus on the side if you have Adobe Page numbers enabled. If the OP is seeing those page numbers on the side, it suggests that they are not using the WebKit-based renderer. If the OP looks at the book in Books view, they should see EPUB as the type for books that will use the RMSDK renderer while KOBO PLUS or KOBO EPUB will use the WebKit-based renderer.
Since calibre removes the double barrelled .kepub.epub extension when ebooks are added to a calibre library, unless the OP was using the KoboTouchExtended or similar to generate .kepub.epub versions to send to their Kobo using Send to Device, what they would get on their Kobo would be .epub versions.
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