After I had updated my old Imac (2008) to El Capitan the file transfer between the Boss BR-600 and the computer failed. I did a lot of tests and research before I finally could solve the problem. I even have purchased another Boss BR-600, because I can not live without one and I thought, that it must be a hardware failure.
To save you from weeks of desperated tries and errors I want to publish my solution:
It seems, that the Boss Wave Converter or the Boss machine is not compatible anymore to the wav-files generated on an El Capitan system. But I found an easy method: AIFF-files still work!
Just use AIFF instead of Wav for Import and Export and the Boss BR-600 works as expected.