EDIT JULY 8 2008: Please read this for the method we recommend.
ORIG POST ON DEC 2004:Ankh, I understand that the intention here is to allow authors
QUOTE
to announce news like 'Such-and-such a story renamed to 'Whatever.' Or 'I have removed this fic. Because …'
What I've seen some authors do is one or more of the following actions:
Post a notice in their profile pages' "author bio" fields. Example:
QUOTE
I have deleted "Hermione's Mission" from Portkey. It has since been through a massive edit, and the version archived here reflected badly on my writing ability.
Delete the story's chapter/s, but leave a note in the summary. Example:
QUOTE("Discipline" fic summary)
After a lot of thought, I've decided to pull this piece from portkey. I don't know why I wrote it, and rather wish I hadn't. Out of deference to my reviewers I'm leaving the marker in place, but I've decided the sotry just doesn't belong here. Thanks to the mods who let it stay up, I know it was a tough call.
Leave a note in their stories' recommendation thread. (Although all of the cases I've seen had the authors replying AFTER we readers contacted them, to ask where the fic had gone.

)
Example: QUOTE
Wow.
First of all I want to apologize. I honestly didn't think anyone would notice or care if I took my story down.
I'm planning on reposting Celebrate but I'm going to go back and clean up any nitpicky errors I missed during the first go-round. I'll be uploading multiple chapters at a time and I'm hoping to have everything back up in a week. The first batch should be up in a day or so.
Thanks again. It's nice to know someone actually remembered my story!
So there are existing means by which authors can inform their readers on their story's disappearance. I wish authors would pro-actively announce such changes on their Rec threads, though.

We Recs and Fic Hunts Mods often get alerted by the readers, rather than the writers, to these changes. In my 15 months of Mod-ing, I can recall only one instance where the writer himself told me (in my capacity as Rec Mod) that he was taking down his story.
Thanks nonetheless for bringing that up. Others must be wondering about that too.