The word is in my Random House Unabridged Dictionary (CD edition), but it's a "Word Perfect" spinoff so it's probably wrong.
I think the misuse of "conflate" to mean "confuse" might come from a book some one wrote that described people who "conflate metaphors" - i.e. mix a pair of perfectly good bits of tripe into a single peace of meaningless tripe. At least that's one of the first places I encountered the word. But I was only about nine years old and haven't the slightest memory of a title or author.
It might also have been that the author was simply confused, as many people have been since, and just wanted a big word to impress nine-year old kids; but I doubt that kids my age were really expected to read that kind of stuff, even back then.