I'm in the process of moving a large number of files. In Windows 10 when viewing the files via SMB shares, the first folder shows over 100K files, and 44K folders, in then second folder just 1 file and 63 folders. When I browse deeper I can see there are definitely more than 63 folders. Both directories have the same ownership, they are the same file system ext4, and they are even the same model of HDD.
And when I do a diff with the options -rs, it shows everything is the same.