Just to clarify, are you referring to the Object>Object Layer Options feature? Can you show us the problem with screen captures?
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As a matter of fact, Controlling layer visibility is quite tricky...
Without any screenshot, especially a screenshot of your Photoshop layers panel, it's hard to advice, but here's information you might find useful:
First of all, after reading your request, it looks like you used "Use Photoshop’s/PDF’s Layer Visibility" instead of "Keep Layer Visibility Overrides". Change that...
Then, I guess that you used Groups in Photoshop layers, and that you select the whole group while placing in INDD.
But you should be aware that the position of the layers is crucial point.
INDD graphic update is based on the original position of the layers, and of course, if you add new layers, the whole thing will mess up...
So finding a satisfactory workflow is up to you, depending on how is your PSD file built.
Here's a live example:
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Save your layers states in Photoshop in Photoshop’s Layer Compositions in the Layer Comp. Panel.
When you place the file in InDesign or Illustrator select the saved Layer Comp. so you are sure that it remains the same if the file content changes.
Were you able to find success with Wilhelm, Rob, or Vinny's suggestions? Let us know if you need further assistance.
… But you should be aware that the position of the layers is crucial point. …
InDesign cannot remember the layer's visibility by its name. Indeed that would be fatal, I think.
The reason why "remember layer by name" would be not possible or a good choice by the developers of InDesign is that in PhotoShop every layer could have the same name. So identifying what's on/off by name is not possible. Unlike with InDesign where every layer has to get its own unique name.
It would be cool if InDesign could remember layer visibility of a placed PhotoShop by other means.
E.g. by something like a unique ID number assigned to a layer in PhotoShop. A ID number that would not change even if you renamed the layer or moved it around the stack of layers. But maybe there is not a thing like that?
Ok. I checked back the ExtendScript Document Object Model for PhotoShop with CS6 and CC 2015 and found, that indeed there is a property named id with a number as value with a given layer. Undocumented with CS6, documented with CC 2015.
Did not test much, but if the value of id would be unique and if it is not used again if you remove a layer and add another one, that ID indeed could be a possible hook to remember layer visibility with files from PhotoShop placed with InDesign. Something we could do as a feature request perhaps. I did not check back with older versions of PhotoShop so perhaps it would be no option with legacy PSD documents below PhotoShop CS6.
However, it could be a hook for a script that checks layer visibility of a placed PSD on base of ID numbers or a combination of layer id and layer name. But that would require to open a PSD in PhotoShop every time you place it or update a link.
Willi already pointed out a solution in post #3:
Work with Layer Compositions in the "Layer Comp. Panel" of PhotoShop.