Ok, I have found that using good ol’ Filezilla to upload new files works.
(Before I had a Sublime Text plugin that was doing auto FTP uploads whenever I saved new changes).
So although I still have no idea how the file exists in the remote, but can’t be accessed – the workaround I will use it to use Filezilla for new files, and continue to use the Sublime plugin to update changes on existing files.
