Yes, it is the file sync in scheduler doing this.  Not only do you loose all files and folder permissoins, but when you resync, it creates new file entries in the files table so anywhere you used skinobjects like Logo and the logo dissappears because it is now pointing to a file id that doesn't exist anymore.

I would love to see something solved on this.  I saw the redommendation about disableing the sycn and using the auto option in Host Settings.  Will that achieve full syncing, even with FTP'd content?

Also, does anyone know of a script or module that can be used to set the folder permissions instead of gonig through each folder one by one?

I cannot reproduce this on any of my 4.8.4 sites, have you checked your event viewer?
Maybe you are missing some stored procedures or even some crucial DNN files in your upgrade.... Might be worth doing a comparison check with a fresh 4.8.4 install.
 

it is strongly suggested not o use Scheduled File Sync. Please disable the job and use auto File Sync in Host Settings instead. If you create /edit / delete a folder from File System or FTP, please perform a manual file sync in Admin :: FileManager (top right corner of the module).