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PDF is destination format--and usually a final destination. It would be hard to imagine a worse source format for conversion. There is no "poof!" The very nature of PDF precludes being "poofed" to anothef format. There's really nothing to be done except diving in and cleaning things up by hand. Regex can help if you're capable, but any such search & replace would have to be tailored to each individual document. There is no "regex X will do Y."
Good luck.
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