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Is there a way to unpack to the original files, bit for bit? Or, is all that original information left aside as the conversion software packs the file into a .mobi archive? Thanks!
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MOBI isn't really an "archive." It's basically a binary database that's compiled from source files. Unless the source is still included with the package (kindlegen produces files which include the source files), it's simply impossible to rebuild/recreate the exact source files "bit for bit." Mobi_Unpack will allow you to extract the markup code that's contained within a mobi file with very little change, but it still won't represent the original source. Using the debug option, you can actually dump the raw contents of the mobi file, if you so choose.
Mobi_unPack.py