The suction cup trick basically only works to help alleviate the pressure in instances where the screen is still touching the LCD screen where there hasn't been any permanent damage. To make matters worse, it's not always easy to tell if it's an easy fix or not, and attempting the suction cup trick can make matters worse. In any instance where the actual liquid crystals of the LCD have been compromised... I don't actually think there is any repair that can be done short of replacing the entire LCD.
Since you were dealing with a screen protector... are you sure you didn't simply manage to trap some air between the protector and the screen? Or have you removed the protector and the 'stain' is there?