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You can access the layers by opening up the Smart Object, they are not gone.

Note that there is a difficult issue with one of your Layers in particular.  If you have a healing Layer, what is placed on the Layer is based on the existing pixels below that Layer at the point in time the healing was done. (based on how you have it set up).  If you go back to the underlying Layers and make changes (e.g in the Smart Object), the pixels in your healing Layer will not track those changes below.  This is not because of the Smart Ojbect, it would happen for regular Layers as well.  It would probably be better to do the healing within Camera Raw when you have the Smart Ojbect open. 

Hope this helps

John Wheeler