Biztalk maps (and XSLT 1.0) can only output one XML file.
Sounds like this is a case for a custom disassembler in a Receive Pipeline
or use some type of C# preprocessor to split the file first.
On this website (BiztalkGurus.com) Stephen Thomas has several examples of debatching, but I’m not sure that applies in your case, but you might get some ideas. Debatching is taking one big message, and breaking it into several smaller ones.
Neal Walters
http://Biztalk-Training.com