Hi Merina,
Develop one custom adapter module to check the mandatory control segment fields. and if any field is missing then populate it with some default value. then after use IDOCFLATtoXML as 2nd module to convert the flat idoc to IDOC XML.
The FLAT IDOC file is fixed length file, hence to introduce any default value in the control segment is easy.
Hope this will help.
Regards,
Suman