have you tried working with your MV VFD vendor? I am assuming you have one sense it appears this is the source of your issue.
in general, I would recommend getting an accurate model of your system including modeling your harmonic injections from VFDs and then determine what you want to use to mitigate your problem. For instance a properly sized and placed reactor used as a choke would be a possible solution. there are many manufactures of MV reactors although they probably aren't advertised as EMI mitigation.