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The problem is that after splitting, ebook formatting is different - ebook was justified before and is not after. Who knows what other (formatting) changes were done?
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Splitting doesn't
try to do ANY formatting. It's simply (well, OK... not really simply) splits the binary container into two parts. Now, that doesn't mean that KindleUnpack isn't at fault, here, but only that its splitting function has no integral format parsing/altering routines.
Some preliminary questions would be:
- The joint-mobi ebook was justified before when viewing it on what?
- Are both resulting Kindlebooks not justified after splitting, or just one (again, viewing on what)?
- Was the original joint mobi an untouched product of Kindlegen/Kindle Previewer or something else?
For the record: I'm not seeing any changes in justification after splitting any Kindlegen/Previewer-produced joint mobis -- in either the KF8 or mobi-only results.