I just spent the past four hours trying to work this one out so posting here to hopefully save me time when I have the same issue in 6 months time.
I’ve got a bunch of files on my unRAID server. For reasons then unknown, all of the files in one of the folders weren’t showing up when viewed in Windows through the Samba share. I could still see them when browsing with Putty but Windows was convinced the folder was empty.
All it needed for a fix was a chmod:
chmod 776 *
Turns out the files had full permissions set for the “everyone else” user and Windows didn’t like that. I’m not really sure why it just hid the files altogether but hey. Sometimes Windows does weird stuff.
So, there you go.