I've had the same problem before, how I fixed this was to rename the existing file on the server before uploading the 'revised' version. Usually just added .orig to the end of the original file. I do this instead of deleting it, so I still have it, JUST in case I want to revert back to it. It IS very possible that it is attempting to 'resume' instead of overwrite, which would cause problems and no changes being made.
Just a thought.
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