After replacing the cpu cooler, we turned the system on with just the psu and hdmi plugged in to see if it works, it did and booted into windows but we had to power it down by holding the off button on the front of the PC to move some cables. After rebooting, the nvme drive is missing from the boot options and won’t reappear (with csm enabled or disabled)
Update: we changed a setting for nvme drives from auto to pcie and that seems to have fixed it