A ghost plot in both senses is the story of how Nearly Headless Nick has died. Rowling has written a ballad about this. The ballad got cut from the book but doesn't seem to contradict it.
See the answer https://scifi.stackexchange.com/a/14588/4918 "Why Was Nearly-Headless Nick Beheaded?". Read the full ballad on J. K. Rowling's old website which also says
In the first draft of 'Chamber of Secrets', Nick sang a self-penned ballad explaining how his head had (nearly) come off. My editor was not very fond of the song and so I cut it. However, for those who are curious, here is the story of Nick's decapitation in his own moving words.
The following two are about plots that got changed, and are no longer compatible with the story, so these don't answer the question as posed.
J. K. Rowling has mentioned her plans for a wizard who gets into Hogwarts without having done magic before, but “who does manage in desperate circumstances to do magic quite late in life”. She's decided against this idea before she wrote Chambers, and we never found out more.
Another ghost plot we know about is that of Mopsus, a blind wizard who is good at Divination, mentioned in a 2005 interview (thanks to DVK).
[…] at one point there was a blind character who went by the name of Mopsus, and I will let you look him up because there is a mythological connection there, but he sort of -- that was a very early character and he had the power of second sight, in other words he was a bit like Professor Trelawney, he was a very, very early character, this was when I was drafting Philosopher's Stone, the reason I cut him was he was too good. As the story evolved, if there was somebody who really could do divination at the time that Harry was alive, it greatly diminished the drama of the story because someone out there knew what was going to happen.
So that is why Mopsus went and I have never really replaced him, […]
