You can try to create a dynamic target and parameterize the flat fie name .While running the workflow provide the parameter file to create a dynamic flat file .
For creating multiple flat file you can use the multiple sequence flows under same workflow which will create multiple flat file .
You can refer to below document for sequence flows :
Thank you .
We can parameterize Target file name and directory to create multiple targets with desired names during run-time in IDQ.Please refer to below document on how to parameterize target flat file name and directory:
Refer to below document on the use case of running dynamic mapping against different sources and targets: