Front suspension/strut adjustment

Passenger and driver side strut was raised manually prior to taking off nut below strut, to gain better access to nut when replacing lower control arms. When replacing new control arm with ball joint, the strut would not return to its original location, thus the wheel well is significantly higher than the tire. How can I lower the strut back to its previous position? Does the floor jack have anything to do with it? If the jack was lowered while the control arm was out, does this harm any thing? Image can follow if needed.