They don't do it for songs, otherwise Telephone would be in the all-time top 50. So I assume they also don't for albums?
They do it for the albums, cause some albums that spend only a few weeks on the album chart still make the year-end chart if they were always close to the top 40 where GaGa will most likely be when she falls off.
They only update the points for the songs on the all-time chart, while they are still charting and even when they fall off the track chart.