The Flat File Disassembler only works from a static schema definition.
Depending on what is changing in the flat file and how it is changing you may be able to use optional records and fields in your schema to cope with the change.
Or you may like to use a generic flat file schema and use a component in the pipeline to call an Xslt from a file to create the output message you need.
Or you could write your own custom disassembler that works from a config file.
Can you give us an example of what is likely to change in this file?