I do think it's probably "safer" to be sending a calibre EPUB rather than calibre KF8/MOBI.
If it was me I'd do a calibre conversion KF8 to EPUB or, as Jon said, KindleUnpack KF8 to EPUB to get an EPUB in my library. I'm pretty sure you know enough about calibre to know the pros & cons of each

Then I'd remove the KF8 from my library never to be looked at again. The thought of relying on KF8/MOBI/KFX as my master archive format makes me shudder, but then again I don't own a Kindle.
Once you've got the master EPUB you can do a full conversion to KEPUB (via Kepub Output) if you really want to clutter your library with KEPUBs or you can use KTE's on-the-fly transform EPUB to KEPUB. The KTE transform is much faster than a conversion because it only adds the horrible (but necessary) koboSpans and a couple of <div> wrappers to each HTML file rather than a complete re-jig of the whole book.