You don’t have to worry about that. The concept is similar to Dropout, you zero the activations in the top layers and as a result the activations are not carries in the previous layers.
Say you have 2 layers. And you apply the mask in the last layer removing 4 neurons from the last layer. During the back prop their activations would be zero and as a result the neurons in layers 1 would be updated by the other (n-4) neurons.
Hope it helps.