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In that case I'm not understanding the question correctly.

CTRL + Click thumbnail creates a marquee based on ALL the pixels in that layer....regardless of transparency (Opacity).

If you then COPY that and paste it you'll find its exactly the same as the original.

What you may be getting confused with is how PS DISPLAYS the marquee......it will only place the 'marching ants' around pixels with 50% opacity or greater.

To test this, click in a new layer with a large soft brush.

CTRL + Click the new layer thumbnail. The marquee boundary will be around halfway between the extremes of the pixels.

CTRL + C to copy the pixels.

CTRL + V to paste the pixels on a new layer.

The two layers should be identical...proving that all the pixels were included in the COPY command despite the marquee DISPLAYING only around those over 50% opacity.

EDIT:

I think the penny has just dropped and I now see your problem......scrub the above, hold the phone...I'll be back!

Regards.

MrTom.