Just to point in the right direction: take a look at lm-sensors and sensors-detect command in it (and read the relevant documentation). ( EDIT: The following paragraph does not apply for the USB fan controller OP is using, but leaving it here since someone might stumble on this thread for who this is relevant) I doubt there is anything stored in the FANs themselves, if you set something up in Linux, it should in no way interfere anything set up on Windows (or vice versa) ( EDIT: in case of the Corsair Commander Pro, this might not apply since it seems to have some kind of internal memory? I'm not familiar with the device, does it store anything between reboots etc.). See if you could get WINE to work and try the Icue software in Linux I really dout that would work Has anyone had this problem before? Any known solution to update the default fan speed values on Windows or Linux?

I'd honestly prefer option 1, so I can have everything on Windows. I've managed to workaround this by booting Windows first, letting iCue change the values (I use 600 when not gaming), then reboot in Linux, but I'd love to either: Having 9 fans at 800 rpm makes the computer too noisy if I am not using headphones. iCue allows me to update the lighting default hardware values (stays after reboot) but not the fan speed, which defaults to something around 800 rpm as far as I can tell. This computer has 9 fans, all Corsair (6 LL120 and 3 ML120), and everything works great on Windows using the iCue software, I can control the fans speed and lighting, but on Linux the lighting and fan speed is set to the default hardware values. So I decided to add a Linux partition for everything non-gaming related. I recently put together my first computer:

Linux compatible fan controller