Hello Mario,
When you have created a datasource for flat file it wont show the OLTP hierarchy as it isnt connected to OLTP OR looking for hierarchy which are available in OLTP. Only in the IP which is having your OLTP has source system will show the hierarchy after you select the button "Available Hierarchies from OLTP"
Also I am assuming your using routines in transformations/tranfer rules to calculate hierarchies and same logic will need to applied in the Flat File related data flow so that existing one gets updated
Thanks
Abhishek Shanbhogue