I have configured a smart setup to be able to change the CONTRL message version per partner.
1. I assume you have a Sender EDI separator channel listening to CONTRL message.
2. I have added: ocalejbs/EdifactConverterModule to the adapter module, this way the CONTRL message is converted to XML.
3. I made a mapping correcting the headers and of the CONTRL message to the one I need. In my case I needed subversion EAN002. You should import to the ESR the version of CONTRL message you will require as target and the standard CONTRL D/3 for the source of the message.
4. In the recever adapter (AS2/FTP/etc) I have added the ocalejbs/EdifactConverterModule module again.
I hope this help you.