I don't fully trust this now, I'll have to go a different way to transfer data, don't have the time to be checking terrabytes worth of data to see if it all copied over correctly and possibly adding duplicates I can't see too.
Just for further info, I did upgrade, rebooted, disk checked the effected disk, still the same, missing files and folders that I done as a mass copy with other files and folders in one go, not individually.