Have you validated the nvme drive externally after it disappeared, to make sure it didn't really die (or become dislodged) coincidentally? They really should have nothing to do with each other, and even if you accidentally repartitioned the nvme drive, it would still show up.
Validating externally aside, you should also check the output of `dmesg`. It is highly unlikely that this problem is due to anything outside of the kernel itself. It is certainly possible that between the boots, you changed kernels.
I've been running dozens of nvme servers for about two years on Container Linux (CoreOS) without similar problems, both with and without PXE booting and with and without other drives (i.e.,, /dev/sda). It is, however, possible that the particular combination of devices you have is causing some internal conflict. If it is not unreasonable, you might try removing the non-nvme drive(s) from the system and see if the nvme drive returns. (This is purely for diagnostic purposes.)
forgot to mention, Im running 1465.7.0 x64
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