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I can not use and see my layers in the "menu layers" in a document where I have used multiple layers.
The first thing I would try is to move or copy all pages to a new document.
Which version of InDesign and OS?
(I assume you're familiar with the Layer panel and the twirl down feature that reveals individual layers?)
Does this issue apply to all documents or just this one?
If there is an application corruption it would be worth resetting the InDesign preferences.