Please be more specific. Versions of ID and AI, PDF options in AI.
Screenshots would also be helpful.
I'm not sure where I'd look for PDF options in Illustrator. I certainly haven't changed any PDF settings... and since the problem seems to be intermittent at least, and perhaps tied to certain documents, I'm at a loss. These documents were all created by duplicating a master doc, so I can't imagine why this problem would affect only some of them. I've had this problem for YEARS, through multiple versions of inDesign, multiple operating system versions and multiple computers.
I only give you the caveats. If you change anything about the layer
structure you’ll go back to the saved state.
I'm confused. I'll go back to the saved state of the Illustrator document or the Indesign document's supposed handling of the Illustrator document. If it makes things easier, I don't EVER want to use InDesign to determine which layers an Illustrator document shows--using inDesign to select visibility like that has zero utility for me. I will always want to default to the Illustrator document's visibility settings.
Are you saying that you don't see that behavior? That despite saving the Illustrator document in a certain state, you're not seeing that displayed?
That's exactly what I'm saying. When the object in InDesign is set to "use PDF's Layer Visibility" inDesign shows exactly the layers that are marked as visible in that dialog--the override settings. I can reset the pop-up, I can reserve the document, I can quit the popup, open it again, change the setting back and forth from override to Use PDF--it doesn't matter. InDesign goes with its overrides. It's not the case for every illustrator document that I've placed in my inDesign document, but neither have I noticed any kind of pattern for the documents which it does have a problem with.