I've had Sync set up for a bit and installed the latest version (v2.14?) today. I haven't fooled with Sync since my Windows boxes updated to the Fall Creators Update, which I have a feeling is behind this schmozzle.
I had a folder share with a number of subfolders that Sync started complaining it couldn't access three of the subfolders. Making it rescan the main would alleviate the problem for a while and then it would reoccur.
So I deleted the share from Sync. I delete the .sync folder in the main folder and restarted the machine.
When I go to create a share of the same folder, Sync indicates that there are three folders that are not in the folder. These are the same three that it was complaining about.
The main folder is c:\users\chris\Documents
The three it says are there, but aren't are: