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For myself, I keep all my reflowable ebooks in my calibre library in ePub format. For those friends of mine who have Kindle or Fire devices, they also keep their libraries in ePub format and convert on the fly when sending to the devices either over USB letting calibre do the conversion or using any of the Send to Kindle services.
Most of them are using either Sigil (ePub editor) or calibre's ebook-editor (ePub or KF8/azw3 editor) though the preference is for ePub in either case which allows using the epubcheck plugin to locate errors—most publishers use epubcheck to locate errors in files sent to them and passing epubcheck is very likely going to make your ePubs acceptable to Send to Kindle.
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