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My question: My device is Kindle so the vast majority of my files are mobi and azw (and those variations). Will epubsplit work on those files and if so, do I need to convert to epub, split then reconvert back to mobi?
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As others have said, converting mobi/azw to epub, splitting and converting back to mobi/azw should work.
But I don't know how well. Conversion changes the contents to some degree. How much and how well depends on the source book and your conversion settings, mostly.
I would not trust a convert-split-convert-back process blindly. I'd try it for a book or two and see how it works. And even after that, you should examine the contents of all the split books you make, not just assume they worked as intended..
Sorry I can't give you a more definitive answer, but I don't think there is one.