This conversation has been merged. Please reference the main conversation: Photoshop CC: Duplicating linked layers containing hidden layers causes them to display in duplicate
This is an issue I was experiencing intermittently for years now, and it always drives me crazy because it would only seem to happen when there was no time for dealing with it. Today I had some time to experiment and was able to reproduce the error.
Open or create a document. Create a layer set. Create two layers inside. Link them. Turn visibility of one off.
Create new or open another file.
Drag your layer set from one to the other.
Notice how visibility of both layers is now ON? Easy enough to fix in this example, but imagine you are working on a complex image and trying to combine two different versions because the client has changed their mind (as clients often do) - not so easy to fix then.
A workaround seems to be if instead of dragging, you use "Duplicate Group" and set the target to another document, this issue does not occur. At least, I have not been able to reproduce this bug today while using that function.
my system specs:
OS X 10.12.4
Photoshop 2017.1.0 Release
Also, you might notice in my screenshots that I'm experiencing that bug where white displays as cyan in the layer thumbnails. That's been going on intermittently for ages too, but it is less of a problem.