A few weeks ago I went on a photographic workshop and took ~8000 photos on Canon 1DX MK II bodies shooting RAW exclusively to the 128 GB Sandisk CFast card without any issues. I always downloaded the photos every evening and reformat the card in the camera whenever I finish downloading.
Based on the discussion maybe this is something that occurs when once records both RAW and sJPEGs to the same card? Sending RAW files to the CFast card and JPEGS to the CF might be a good workaround although it is not ideal.
Good luck,
John