They're not hidden files and I have the preference to Show Hidden Files. 
 
Well....I have 2 folders that I know that look like they're "broken" this way but I haven't checked every folder to verify. 
 
The files within those 2 folders that are missing missing files seem to be the same ones every time I open up FlashFXP if that is what you're asking. 
 
They show up fine if I use FlashFXP to connect via FTP to that same server or if I just use the Windows Explorer.
		 
		
		
		
		
		
		
		
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