Yes its safe , but ..... Clearing a blocked drain is just that , clearing it , the water is already in the motor casing . The roof motor is inside a plastic container/casing which is split half way up,this casing sits down in the drain pan just on top of the drain hole . The casing sitting on top of this drain hole helps cause the blockage, if the drain blocks up with leafs and other debri over time then flooding of the motor casing will occur .When the drain gets blocked the water level in the drain gradually rises until it is higher than the motor casing joint , where it then floods the casing . Once it's in, it can't come out and causes the motor failure . You'll need to do more than just clear the drain as this won't release any water in the motor casing .