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My recommendation for epub --> mobi/kindle in linux would be to use the command-line kindlegen program (available for linux natively), especially if you intend to distribute the kindle version. Note that Kindle previewer uses this same kindlegen back-end for its conversions.
FWIW I have been making commercial epubs (and mobis) from word docs entirely in linux for years, using the tools discussed above and elsewhere on MR. I only need Windows when InDesign is involved. (OK, and also to preview the finished products in ADE and Kindle Previewer.)
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