When I go to change my quest in Diablo 3, I get a prompt telling me "Starting a new game with a new quest will overwrite your currently saved progress". What will be overwritten? My checkpoints? Waypoint access? Achievements? Whether or not I've killed Diablo?
Where exactly you are in the current quest. For example in ACT 2 when you need to get the two bloods, if you get one blood then quit and save. When you come back you will only need to get one blood. If you change quest, and then come back you will be back further and be required to get both blood.