If you change the light cycle both plants will be affected...If you wish to flower one of them before the other...simply remove it from the light after 12 hours and place it in a dark place....but leave the other plant under the light to complete its veg...this is if you only have one light for your entire grow...also you might want to 'TOP' the tallest one to make it grow shorter and bushier....assuming you are growing 2 seeds from the same strain...it's possible one plant is showing phenotypical characteristics of a satina parent and the other is showing the traits of an indica parent..which is common in sativa/indica cross's