I am currently plotting the three hard drives with gpuplotgenerator and it seems pretty reliable for the moment. I think the issues I had previously was maybe due to third party app to acess a ext4 partition on Windows 10.
So, for this time, I booted Ubuntu mate from a usb key and have been gernerating plots with an average of 28000 nounces / minute, 3 plot files at a time, 1TB each. In the end it is going to take around 40 hours to fill the 3 x 6TB hard drives.