In our convention, we're using the "Message" concept in both cases and use an attribute to sort the "technology" used for transferring.
If end-users needs a hint about the nature, we may add free shapes on the diagram (a group around the relevant messages and a small XML icon inside) to make it clear that some messages are transmitted by file transfer.
When the message is going through a middleware, we can represent it by two different messages in "technical view" : one AppA-->Middleware and one Middleware--> AppB. It's fine beacause "technologies" used in the two halves may be different.
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