The movie should normally be removed from the list when you rename. There is a slight delay when saving movie posters before the name is removed. There is also a bug where sometimes, due to some complexities in how I try and speed things up, a movie might skip or get choosen twice. I need to resolve this bug, but clicking a movie in the list usually resolves the problem and movies are removed as they are renamed.

If you do not use the TT# in the filename as is recommended, then when you hit Refresh on the files, renamed files will reappear. This is one reason it is recommended to put the tt# in the filename.