When moving one layer through frames, it erases other layers in the animation

As the title says, in my animation I am moving clouds through the sky and the clouds are in layer 2 and 3, the sky is layer 1, some mountain ranges on layer 4 and 5, when I animate to move the clouds I have to go through all 256 frames to move it 1 pixel at a time as that is the width of it, whenever I do this though it erases the top half of the entire project, except for the clouds I have just moved, when moving them and selecting them I have made sure to use the marquee tool in the layer that the cloud is in, but it still effects the other layers for some reason, I have tried to just push through but the error keeps happening and going through all 256 frames every time is getting very time consuming and useless