There are few likely possibilities, depending if it was just a fanfiction, or a translation. You see, Tony recently cracked down on both unauthorized translation and fanfic monetization, since both is a potential load of legal trouble and both are against the site rules.
1. The author was attempting to evade donation link detection, so the story got taken down and author likely banned.
2. The author took the story down himself after Tony made it clear he won't tolerate monetization on fanfics - this would show as "deleted" in reading lists. There are a lot of fanfic writers who never read the rules, and then threw a tantrum, or just looked for greener pastures.
3. It was a translation that got taken down, seeing as most of the translations were fanfictions.