We recently had this problem in our lab. No matter what we tried, we could not get convert2mtz (or any other program) to work properly. We were probably doing something wrong with the fortran....?
Depending on how far along you are, you can try using phenix.refine. Just input your model and the .cv file and phenix will export a new .cv file with Free-R flags intact. If you aren't to the model building stage yet, this won't work however.
