I've not got rules to hand but in the original game this was the case. All the age III events were "impact of....." and gave bonus points. Any events from age II or I if still in the event deck would be things that only mattered during the game and not needed to be evaluated at the end.
edit - I'll try and explain this a bit better with a dash of theme! Yes you are correct, it is possible that age II events mights still be in either event deck, but they do not need evaluating. They are just things that thematically never happened. A Colony that maintained independence, a crime wave that never happened, no economic progress, wonders never ravaged.
Many of these age II cards will not affect scoring. Only a few will effect scoring directly and some might do if impact of Colonies has been played for example. once the game is over most the effects, Such as gaining food or resources, won't be a factor.
The end of the game bonus points represent the 'Impact of...' things on the world. Not what is seeded to happen in the future as in game terms that future never got around to happening.