I think the easiest way would be to debatch the file into 3 separate files. I really have 3 files in one. You can do this using an envelope but probably would require a 2nd pass through BizTalk. You could also use an Orchestration to break up the message once you have it in XML.
You could probably also change your schema to support multiple files by adding a higher level root record. But in this case you’d need to redo your maps.