Invisible layers will magically reappear when an Illustrator PDF is loaded in certain non-Adobe products (for example, the Mac PDF reader Preview). To avoid this issue, deselect “Preserve Illustrator Editing Capability” and “Create Acrobat Layers from top-level Layers” in the Save Adobe PDF dialog that pops up after choosing Save A Copy… from the File menu in Illustrator.
xcorr: AI & neuro 
3 responses to “Hidden Illustrator layers show up in PDF files when reading in non-Adobe Reader: solution”
This is great thanks. I did notice, however, that this removes certain effects such as a Drop Shadow on text if it overlaps. Not on the PDF – but through the 3rd party viewer. Any suggestions?
thx a lot for a very handy tip
Great tip… been driving me crazy. Thanks.