When re-import a PSD file with layers turned off or on in InDesign, I get a message that says "...psd has differennt layers than the imported version. The link will be updated with the source file's current layer visibility settings." Is it possible to import the PSD file preserving the layer visibility as definied in InDesign?
I'm guessing you're seeing that message when you go to update the modified link.
If you set the Update Link Options to "Keep Layer visibility Overrides" before hand under the Object Layer Options that should work for you.
Check your InDesign Preferences
Last option in the screenshot
Best way to keep layer visibility is to work with layer compositions.
Any other method of manually selecting layer visibility causes problems if later work is done in Photoshop. If you add or delete layers, take care that the different layer comps are updated correctly.