Moisture in the roofing system is bad. It attacks a roofing system in many ways. It works its way down to rust or rot the deck. It turns into gas when heated and attacks the seams, penetrations and other weak spots trying to escape and causes earlier failure. It freezes in the cold and lowers the thermal resistance, increasing heating costs. The freeze/thaw can cause excessive shifting of the waterproofing layer causing earlier failure. If moisture is in a roofing system it should be removed. However, a cost saving approach can be taken to remove just the layer or area that contains the moisture.