Aside from the fact that fans would of course choose her encyclopedia over a fan-produced encyclopedia (or buy both), it doesn't sound to me as if the books will be similar at all. The HP Lexicon is simply a compendium of information about the books: characters, objects, magical creatures, timelines. There's nothing new in it that couldn't be looked up in the books themselves, it's just all put together as a reference.

But from the statements JKR has made about her forthcoming encyclopedia (which is probably years away), it will be a compendium of things left out of the books -- storylines that didn't fit in, historical background that wasn't covered, future lives of the surviving characters, and various other ideas that didn't make it into the text.

JKR's statement on her website says that fan encyclopedias will take away money from the charity she's planning to give the proceeds to, and I believe that is her main concern, since she hasn't had any problems with previous fan books that were merely analysis of her books. But I just don't see how the HP Lexicon would have any impact on the sales of her encyclopedia when they would have such different contents.

Well said. However, I am sure other authors are watching this case closely. Copyright and the moral right to one's intellectual creations is such a messy arena.