I recently upgrade from Lightroom 5.4 to 6. I realized today that some folders are just missing. I tried to synchronize these folders but this fail. In import windows all pictures are there but shown as "This appears to be a duplicate of another photo already in catalog".
I was also surprised to see that the old version of Lighrooom 5.4 was still there and in that version all folders are shown
Sorry that some folders are missing in Lightroom after you've upgraded to Lightroom 6
Are you able to find the actual operating system folders by searching in Explorer/Finder?
Can you search in Lightroom for the file names of some of the photos in the missing folder to see if they are already in another folder. make sure you have your entire catalog selected in the left hand panel?
If it says it is a duplicate, then you need to find the "non-duplicate" copy of the photo in Lightroom. Click on "All Photographs", then search by file name.