It is the file adapter that is discarding the message before being given to the pipeline. Creating a schema will not help as this is not used until the disassemble stage in the pipeline.
You will need to create your own file adapter, for both receive and send.
If the file is empty you need to create a dummy message, with a message context property that indicates that the file is empty. When the file is sent you will need to detect that if should be an empty file from the message context and discard the dummy message content