I'm pretty sure it's just a technical thing to do with how they treat each chapter uploaded to the site as being a "story" (this chapter of HPatEC is story/252122 and is the 252122nd chapter uploaded to the site, rather than having a sequential storyid or title and then a chapter # like ff.net or hpffa use) and updating how their catalogue and retrieval system works. When it says "this story has been deleted" it's only talking about the blank title page "stories" that were only being used for collation or whatever.
I think they are just trying to update the site's functionality to make it less awkward, they aren't just going around deleting literally everything (at least not on purpose) and I don't think anything has actually been lost yet or expect anything will be.
This story has been posted on hpfanficarchive up through chapter 18. I don't know if that wasn't actually you or if you just stopped updating there for some reason or forget about mentioning that as another alternative place to find it besides here and ffn but it's always seemed to be a stable site and they only seem to delete stuff when it's being plagiarised rather than purging smut like ffn.