When you export a PDF from Adobe InDesign and choose the "Create Acrobat Layers" option, the resulting PDF file contains all the layers from your INDD document, placed in a "nest" structure with the document filename as the heading. Along with the layers you have created in your document, InDesign always adds the "Guides and Grids" layer, even though there is usually nothing in it.
- It promotes all layers inside the nest to the top-level, and deletes the nest.
- It unlists the 'Guides and Grids' layer from the sidebar panel - the layer is NOT deleted, but it's no longer mentioned.
The document structure is not changed - layers are not flattened, and any layer properties are retained.