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Word is the worst thing you can do to an eBook. But because you've made the choice to infect your eBook with Word, you'll just have to deal and clean the infection that is Word when you do convert to ePub.
And yes, you do have to convert to ePub. Then from there, you take the ePub once cleaned up after being converted and you convert to Mobipocket. But you will have to clean up ALL the infection that is Word before you convert the ePub to Mobipocket.
This is not the ideal solution, but given that it's probably too late to do it any other way, you'll just have to spend a good amount of time cleaning up after Word.
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