I asked once why reworking a fanfic story for publication means you have to pull the original story, and someone who's done that told me "it's not logic that matters. It's business.

Actually, I can deal with the whole "my publisher made me do it," excuse, because if I can buy the fic as a book, I can still read it, just as I can accept the "I received a C&D letter" one or the "I've been outed at work and need to conceal my fannish activities before I'm fired for writing slash" one. It's the "I just didn't want people reading it anymore because I'm in a new fandom/tired of it/throwing a hissy fit over something that happened at fandom wank/re-using minor plot elements in fics for a new fandom and/or orig fic with completely different characters" that makes me want to scream.