I have noticed that sometimes there are changes made to games which cause gaining a high score easier or harder. Therefore I think it would be more fair if after such changes a new score table would be started. It could be done on every version change or AG could open polls on that per game. Another possibility is to give developers a means to indicate such a change (then again there are several ways how staff or people could decide how to proceed).
I haven't said that the old scores should be deleted, they could still be archived and be accessible by version number. Another approach is to store all versions (at least each last one before a major change which would justify a new score table) and let people play their preferred one.