When using hidden options, the nested options will disappear when deselecting the controlling parent option. However, the hidden options image will still show on the Image Customizer. This can be fixed by setting up the layer to be controlled by both, the parent and child options.
In this example I will be using the Grid option as the parent option, and the Pattern and Color option will be the child options.
This tutorial does not cover how to set up the Image Customizer or creating layers. If you have not done this yet, I would recommend reading the Getting Started tutorial prior to this one.
If after creating an Image Customizer on a product and creating a layer for the Child option Select the child options layer setup in step 2 of the Image Customizer. Choose Both the parent and child
In step 3 when assigning images to the layer you will need to choose which image to show according to which option is selected. When choosing an images, on options with field values equal to the parent field you want to hide the child options. Simply assign the image to show as none. This will remove the child images nested under that option but still display the others.