Reply To: Automate change object layer option

At the bottom of the Object Layer Options dialog box in InDesign, there is an option for “When Updating Link”… that should let you control what happens when the file updates: either keep the photoshop layers or keep the layer overrides.

More info here (the article is about illustrator, but it’s the same mechanism)

Changing the visible layers for Illustrator documents

and this preference may also help:

A Fix for Problems With Layer Visibility Overrides In Placed Illustrator Files

and this script won’t help you directly, but it’s cool:

A Script to Change Layer Visibility of All Instances of a Placed File in InDesign