We have a share set up on a Windows 2012 Server that it accessed regularly by users on Mac OS X El Capitan desktops. At initial opening, these folders are complete, meaning the users see all the folders and files in the share. But after a while, it seems that the Mac will refresh the folder contents, except it only loads a portion of the folders. The only way to get the directory to show all folders/files again is to wait (usually 5-10 minutes), or to re-launch finder.
Initially, I thought the share had too many files/folders and the Macs were having trouble loading up the entire directory, so I split it in two, A-K, and L-Z folders. But the problem persists. At initial opening of the shares, the folders are complete. Then the "refresh" happens every so often and it will sometimes only load a portion of the files/folders. The user is logged into the Mac on a domain account, has full permissions to the directory (in Windows (Full Control) and in Mac (Read/Write). Account is not locked and is in good standing. I'm not sure where to look next for the cause of the problem.
Only other clue I have is, if the user is accessing one of the files in the share, \\server.domain.com\a-k\example\example.pdf, and during the refresh, the a-k directory only shows folders titles f-k, the file example.pdf that was open does not close. It remains open and active. So even though finder isn't showing the entirety of the folder, the files and folder still appear to be accessible.