I found a hack-y way to work around this problem without losing work!
So I discovered fairly quickly that this is an unsolved problem that NO ONE can explain the cause of. Here are step-by-step instructions on how to save your layers without losing progress.
- Convert ALL of your layers to a Smart Object.
- Right-click on the Smart Object
- Click "Export Contents..."
- This opens up a Save As... Window, with your file name .PSB
- Name & Save.
I then quit Photoshop CS, re-opened, and had all of my layers, folders, and effects intact. The only problem was that my Canvas was as large as my biggest layer (extending beyond my original canvas). Just find the original background layer (or one that originally filled your canvas), Select it (Command + Click on the Layer thumbnail), and Crop it (Image > Crop).
Hope this helps.