You seem to be confusing layers in your protocol stack. The protocol and service you use for exchanging files has nothing to do with whether the files contain XML, so you are asking on the wrong forum.
There's a vast range of approaches you could use, from distributed filestore to FTP to HTTP to asynchronous messaging services to Java remote procedure calls; and no information in your post to enable one to recommend one or the other.
Michael Kay
http://www.saxonica.com/
Author, XSLT 2.0 and XPath 2.0 Programmer's Reference