As long as you’ve navigated to the right folder on FTP it should show all the files that are in there.
I have however found that the online file manager doesn’t always show all files correctly (I think its a caching issue myself)
Its also possible that if a file has been deleted, but you’d visited the page previously, that the page is cached.
If you think the file might have been deleted its worth reading:
Are you using a CMS (such as wordpress) that might be creating some empty folders?
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