Hello Shan,
Here's another way with pure BizTalk – no .NET coding required.
My assumptions:
A FlatFileSchema is defined to process the input flat files. This schema is used to define the receive pipeline flat file diassembler (Document Schema). And, there is one send shape in your orchestration(s) where you output the XML equivalent of the flat file.
Solution:
1. Another Send shape needs to be added (to produce the same flat file data) which specifies a Send Pipeline. The Send Pipeline should have the same schema (as above) as the assembler (Document Schema). You may need to have the output filenames specifed as %SourceFileName%.
Good Luck !
NNdM