Strange Issue when Exporting Artboards as PNGs (Won't Include Layer)

As a part of my usual workflow in Illustrator CS6, I export a series of artboards as PNGs. The two layers I export are called "Content" and "Callouts." Neither is locked, and nothing is hidden. I've never had issues before, but today when I tried to export, Illustrator would only export the "Callouts" layer no matter what I tried. I made sure all layers were unlocked, I saved as a new document, combining the layers, I restarted my machine, I copy and pasted all the content onto a new layer—still nothing, that layer simply won't export though there appears to be nothing strange about it and it's worked in the past. 
However, when saving as a PDF or saving for web, the "Content" layer does show up. Because I'm exporting a lot of PNGs, it's not convenient for me to save for web one by one, so this isn't a viable long-term fix. I'm at my wits' end here. Any insights?
Thanks in advance.
Edit: One thing to note, is that when I tried to merge these layers through the panel's dropdown, it said "cannot merge because the destination is locked or hidden." However, when clicking on options for that layer it doesn't show that it's locked OR hidden.

He meant to doubleclick on a layer and make sure a checkmark is in front of print.
Do a view >> overprint preview, if the graphics dispaear thatn menas you have for example somehting white set to overprint. That can be fixed with the attributes panel, by selcting the offending objecy and removing overprint.

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