Are you talking about fanfiction.net?
As impossible as it is that the actual author would be looking at fanfiction, it sounds just as unlikely that a person would be able to get into the site to remove or change things, or even come up with enough of a case that they could get someone's work deleted.
Do you have anything so much as a screenshot, or examples of stories that are no longer there? Do you have a text communication of this person making such a claim? An exchange where someone announced that they had removed stories or given an explanation as to why they had done so? Does this site even have a process for requesting a story be removed? Are you sure the author couldn't have taken it down themselves?
You may not have been trying to instigate anything, but you gotta at least show something, otherwise this sounds like nonsense.