Are you sure that calibre is not syncing over the Mobi version; take a look in calibre | Preferences | Advanced | Plugins | Device Interface plugins | Kobo Reader Device Interface and ensure that mobi | azw | azw1 | azw4 are not selected.
To be really sure make sure that it's only ePub and pdf selected.
Also, while the Kobo is attached, why not take a look at the directories and files on it, and ensure that the ePubs are present.
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