I once converted endnotes in Word to footnotes in WordPerfect (including the automagic codes to make the footnotes refer back to other footnotes/pages by number). Which was hideous.

And then the author *kept sending me line edits every single day*, which needed to be hand-entered *by me*, because otherwise I'd have to run the conversion all over again!

(This was for a law review article.)

Sorry, bad flashback there. In short: authors getting the footnote/endnote thing wrong: very bad for so many reasons.