Your Nutrition Facts was calculated on the data you entered and your weight goal. If you selected to lose 1 pound per week, then yes, Your Nutrition Facts deducted calories to include the weight loss. No guesses here. Healthy Body Calculator® is based on your physical measurements and nutrition science algorithms.
The only variable you are asked to estimate is your activity level. Make sure that you have accurately estimated your activity hours. If your weight loss does not occur as expected and you have kept track of the calories you have eaten daily, you may want to go back and re-assess your activity level. It may not be as high as you estimated.