Why not simply add pdf to the file types that can be sent to your ereader to prevent an attempt to convert on the fly. If you click on the ebook in your library and tell calibre to convert, then that's on you but since conversion leaves the original, you could just delete the converted version. I've attached samples of the configuration for my Tolino and Kobo ereaders from the Configure Device menu.
Arrghhh... Kovid replied while I was creating my reply!
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