I need to add this....
If you transfer new files to the empty folder the files will appear in the empty folder next time you connect cell phone to PC.
Another note....
All this began after I changed the battery in my Nexus 5.
SOS HELP!!!
I am having the exact same issue. I have this to add. My Nexus 5 has 2 user accounts. My wife is the primary account which my PC can see folders but no files and my secondary account where I can see all files and folders.