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Somewhere recently Kovid posted a message stating that conversion to MOBI, and then convert that MOBI to EPUB, can have good results for some books when you need to remove mark-up. Apparently MOBI has a fairly thorough, but simplified, set of keywords so it allows a pretty rigorous "dumbing down" of complex ebooks. Of course, you do loose some of the more complex layout.
Hope this helps.
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