How much lower are your bars after flipping the stem? If you just flipped the stem without movingn spacers from top to bottom, that could be a huge change depending on the angle of the stem. If you want to get to a lower position, start by manipulating spacers (if you have any) to get lower gradually over time. You should be able to flip it at some point and not have much of a difference in bar height. If someone has cut the fork short, the spacer thing might not be possible.