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Where are you placing the books on your Clara HD? In a separate directory in the root of the exposed partition? Inside on of the Kobo created directories? I have my sideloaded books stored in a directory called with great originality, eLibrary in the root of the exposed partition and have never lost one when doing a sign out/sign in.
As for placing the correct format back on the device? I store epub format only in my library and create kepub or azw3/KF8 format on the fly as/when needed.
If you have the configuration in the KoboTouch or KoboTouchExtended driver set up correctly, you should not be needing to choose formats. For me, I have the KoboTouch driver set to send epub, the KoboTouchExtended to send kepub and the KindleTouch driver set to send azw3 as the primary format with the latter two doing conversion from epub.
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