This odd renumbering of list items seems a bug: https://indesign.uservoice.com/forums/913162-adobe-indesign-sdk-scripting-bugs-and-features/suggestions/38218423-scripting-graphiclayeroptions-changing-visibil

I solved my problem – partly but enough for me. A little adjustment to the LayerVisibility script worked for me.
Just go to InDesign and set a particular layer current. Then run the script that you filled with the two PhotoShop layers that should be present in all images (ignoring any other that might be there) and run it. That script works fine with a little more handwork than I hoped for, but it beats manually modifying each InDesign Object Layer Option.

Main();

//
// set layers on/off in an image or images on one InDesign page
//
function Main()
{
var page, placedFile, links, layer, i, j, k, doc;
var doc = app.activeDocument;
var curLayer = doc.activeLayer;
var pages = doc.pages

var checklist = [];

var PSlayernames = [ “extreme”, “subtle” ];

/* ——————————————————————————————————-
ABOVE IS WHERE YOU ALTER THE LAYER NAMES:
After the words “var layernames” there’s an opening square bracket , then some sets of text enclosed in quotes sperated by commas, and at the end, a closing square bracket.
Delete all of the text and the commas separating it, and in its place put in any layers that you want.
For example: If you have three layers, ‘red’, ‘green’ and ‘silver’, then in the brackets put in each layer enclosed in quotes and seperated by a comma, as such: [“red”, “green”, “silver”].
Make sure they are all double-quotes, not single quotes, and make sure they are ‘straight’ quotes not ‘smart’ quotes.
To ensure that it’s properly formatted, only edit the script in a generic text editor (such as Notepad on Windows, or Text Wrangler on Mac).
DO NOT use a word-proccesing program such as MS Word or InDesign, as that will add formatting to the script and it will not work properly.
——————————————————————————————————- */

var ilDialog = app.dialogs.add({name:”Image Layers on/off on ” + curLayer.name, canCancel:true});
with (ilDialog)
{
with(dialogColumns.add())
{
with(dialogRows.add())
{
staticTexts.add ({staticLabel:”Check image layers to show, uncheck to hide on “+ curLayer.name});
for (i=0; i < PSlayernames.length; i++)
{
with(dialogRows.add())
checklist.push (checkboxControls.add({staticLabel:PSlayernames[i], checkedState:false}));
}
}
}
}
var numChanges = 0;
var imageChange;
if (ilDialog.show() == true)
{
// find all images by their links and process them one by one
links = doc.links;
for (i = links.length-1; i>=0; i- -)
{
// get the file info from the link: stored as “parent” of the link
placedFile = links[i].parent;

// file must be an image, not null and made by Photoshop
if (placedFile.constructor.name == “Image” && placedFile.itemLink != null && placedFile.itemLink.linkType == “Photoshop” )
{
imageChange = false;
if (placedFile.itemLayer == curLayer)
{
// check layers names defined for change and see if this name corresponds witrh the Photoshop file layer
for (k=0; k < PSlayernames.length; k++)
{
// find Photoshop layer byt that name in the image. If it does not exist, the layer will be invalid
layer = links[i].parent.graphicLayerOptions.graphicLayers.item(PSlayernames[k]);

// if layer exists, and if its visibility is not according to checklist in dialogbox, change it to match set visibility (if correct, don’t bother)
if (layer.isValid && layer.currentVisibility != checklist[k].checkedState)
{
layer.currentVisibility = checklist[k].checkedState;
imageChange = true;
}
}
// count the number of changes made
if (imageChange)
numChanges++;
}
}
}
alert(“Done, made changes in “+numChanges+” images”);
} else
{
ilDialog.destroy();
}
}

I’ve cut it down to a script that has part 1 that just displays the info I need (writes it to the console – you you may need to open the script for editing to see the console). Part 2 attempts to reset visibility of all PSD layers to off.
Part 1 runs without problem and does show the info I need.
Part 2 is mostly a copy of Part 1 but suddenly finds a PSD layers object that doesn’t exist anymore (why?) and occassionally brings InDesign in a loop that can only be aborted by stopping the application via Task Manager. Very odd.
Part 3 (to add) will repeat part 2 but when InDesign layer name = PSD layer name, set visibility true. In the end only part 2 and 3 are required for the script obviously.
But somewhere it goes wrong in Part 2 and I don’t know why.

Main();

//
// show ID layers and PSD layers
//
function Main()
{
// ========= PART 0 – VARIABLES DEFINITIONS =============================

// define all variables upfront so their scope is the entire main function
var placedFile, links, PSDlayers, PSDlayer, i, j, k, doc;
var docLayers;
var IDlayer;

doc = app.activeDocument;
docLayers = doc.layers;

// ========= P ART 1 – GET THE LAYER (NAME) INFORMATION =================

// get names of InDesign layers
$.writeln(“InDesign layers”);
for (i=0; i< docLayers.length;i++)
{
//docLayerNames.push(docLayers[i].name);
$.writeln (” “+ docLayers[i].name);
}
$.writeln(“—-“);
$.writeln(“PSD layers”);

// find all images by their links (working backwards) stored in InDesign and process them one by one
links = doc.links;
for (i = links.length-1; i>=0; i–)
{
// get the file info from the link: stored as “parent” of the link
placedFile = links[i].parent;
IDlayer = placedFile.itemLayer;

// file must be an image, not null and made by Photoshop
if (placedFile.constructor.name == “Image” && placedFile.itemLink != null && placedFile.itemLink.linkType == “Photoshop”)
{
// layers of PSD
$.writeln (“File on ID layer: ‘” + IDlayer.name + “‘ has the following layers:” );
PSDlayers = placedFile.graphicLayerOptions.graphicLayers;
for (k=0;k< PSDlayers.length;k++)
{
PSDlayer = PSDlayers.item(k);
$.writeln(” ” + PSDlayer.name );
}
$.writeln(“==== “);
}
}

// ============= PART 2 RESET VISIBILITY OF ALL LAYERS WITH SAME NAMES FOR PSD AND InDesign ======================

// Reset visibility of all PSD layers with same name ID layers
links = doc.links;
for (i = links.length-1; i>=0; i–)
{
// get the file info from the link: stored as “parent” of the link
placedFile = links[i].parent;
// IDlayer = placedFile.itemLayer;

// file must be an image, not null and made by Photoshop
if (placedFile.constructor.name == “Image” && placedFile.itemLink != null && placedFile.itemLink.linkType == “Photoshop”)
{
// layers of PSD
PSDlayers = placedFile.graphicLayerOptions.graphicLayers;

// per PSD layer check if a match is made with ID layer
for (k=0;k< PSDlayers.length;k++)
{
PSDlayer = PSDlayers.item(k);
for (i = 0;i<docLayers.length;i++)
{ $.writeln(“ID layer = ” + docLayers[i].name);
if (docLayers[i].name == PSDlayer.name)
{$.writeln (” Found same name PSD layer (reset): “+ PSDlayer.name);
PSDlayer.currentVisibility=false;
}
}
}
}
}

// ============= END OF FUNCTION MAIN ==============================
}

I may be looking at the wrong place but Edit>Preferences doesn’t mention layers at all. And I’ve read that “Keep layer option” finally seems to work for Illustrator but not Photoshop.
And indeed… layer A and B both had the same psd image with photoshop layer A and B enabled respectively. Close file, open file… links update… all become psd layer B. This really sucks!
I’ll have a look at the FB group – though nowhere do I find an object layer reference in InDesign’s object model so I don’t have my hopes up.

Ploughing on some more psd files seem to retain their layer setting in InDesign. Some don’t. Some weeks ago I did indeed add layers and that confused InDesign completely (some message like “psd modified – now using psd settings”) and screwed up my setting. I believed, incorrectly, that when you set a layer in InDesign it should not matter what changes in the psd, it should keep selecting the specified layer (problem only if that one no longer exists).
I’ve since used a macro in photoshop to create both layer groups with some handy settings that I modify for each image. So adjustment settings change, layers remain and are not added/removed afterwards. That indeed seems to keep the layer setting in object layer options. So let’s hope it remains this way.

Still… I am interested to know/be able to write a script that does what I want (set object layer option explicitly for each image on each page). I would think this a no-brainer but cannot find anything on object layers in the object model as far as I looked.