These files I have in the root are visible in samba, and yeah I have guest login option enabled. I mean that the disk doesn't display all files, even when it's connected to PC directly via USB connector.Files in the root directory of a USB drive will not be visible via Samba (regardless of the filesystem being used) unless you have allowed "guest login".
But I guess I will need to format disk again and download those video files form trackers again, at least it's not important data, I use this disk only for movies