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This sort of thing can be automated using a script.

What version of Photoshop are you using?

Does your pdf contain layersets?

Is the persistant layer the same for each psd you want to do this to? (same position)

Do you want all other layers saved to png with the persistant layer or just selected layers?

Where do the new PNG's need to be saved, same location as the main psd or a relative location?

 

I could try to put something together if you could supply answers to the above.