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How was the MOBI formed?
I would expect you should get a master EPUB that can then be processed by kindlegen to directly create the final MOBI for submission to Amazon. If you can get ahold of that master EPUB, you should be able to apply targeted fixes to the unpacked HTML and then simply reconvert using the same process your professional used.
Tables are... problematic in general, and particularly in the legacy MOBI format. There
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