Lightroom 5.4 changes not saved after touching up in Photoshop CS6

I'm using Photoshop 5.4 and Photoshop CS6, licensed via CC.  My workflow includes Lightroom edits that apply to an entire group of photos (white balance, colors, lens corrections, etc.) followed by an individual export to Photoshop CS6 using the Edit in Photoshop menu option.  Once opened in Photoshop, the changes in Lightroom appear to be applied.  After applying some manual touch ups to the photo, then saving, the resulting .tiff file loses the Lightroom edits.  The original .nef file contains the Lightroom edits, but not the touch ups; the .tiff file contains the touch ups but not the Lightroom corrections.
How do I resolve this?

In Library, set your sort order to Filename instead of Added order and see if the files show up, then. 
How are you doing the Save in PS, using Save or Save As—one will show up, one won’t, I think, but I don’t remember which.

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