The issue I am having is related to the PopCornHour NMJ (Network Media Jukebox).  The system scans my UnRaid drives for media (albeit very slowly) and writes movie/tv info and coverart to the database.  The problem is that per a suggestion from the creators of the database scrapping program, if you want it to skip a scan of a specific folder or folders you put a file into this folder labeled  .no_all.nmj  Now the problem with this is that UnRaid just hides/removes the file and the NMJ database program cannot see it.  Reading up on linux it seems that when you create a folder with a period ( . ) in front of it, then it is hidden.  Is there anyway to fix this or do I just have to deal with it?

It is only hidden from a trivial file listing. If you use "ls -a" instead of "ls" then it will show all files if you're at a unix command prompt.