I think I may have figured something out. If you merged clips and then did a copy project Premiere Pro can't seem to make the link from the merged clip name to actual file name. I figured this out by importing a sequence with some merged clips and some not into a brand new project. The new project did not contain any of the merged files! It displayed them on my sequence time line, but did not import the file. However, any clips on that same timeline that were not merged did get imported into the project.
One more strange thing, in my original project, if I did 'F' for matchframe on a NESTED sequence, it would properly display the clip in the source window. But if I drilled back down into the sequence and did the exact same thing I got nothing!
I would like to do a test with a copied project wherein I select the option to change file name to clip name - I have a feeling that will allow me to match frame. But for now I have a live project going and I don't want to take any chances 
I know that this didn't solve any problems, but possibly it pointed to the cause - maybe?