M.2 SSD disappeared from Windows, can't install Windows 10 version 1703

I have a new Fujitsu D957, which comes as standard with an M.2 SSD. The company I bought it from have added, at my request, two SATA SSDs and configured them in RAID-1, and made Windows 10 Pro boot from that drive array.

When I received the machine (yesterday) I opened Disk Management and saw that the M.2 SSD was mapped to the drive letter D. I am planning to use this drive later on, but to start with I just wanted to make sure that it wasn't being used for anything else, so I removed the drive letter.

I went on to run Fujitsu's DeskUpdate software, which updates drivers and the BIOS to the latest version. I also manually downloaded and installed Intel Rapid Storage Technology from the Intel website, so that I would see and RAID warnings in Windows.

I now have two problems, which may or may not be related.

1. The M.2 SSD is no longer listed in Disk Management!
2. I am unable to install "Feature update to Windows 10, version 1703". I get the following error:

0xC1900101 - 0x20017

The installation failed in the SAFE_OS phase with an error during BOOT operation

I have now uninstalled Rapid Storage Technology, but it hasn't made any difference. What should I try next?

[Edit 1]

Some progress. I checked the BIOS and the M.2 port was set to disabled, and also there is a setting called "M.2 NVMe Storage Remap" which was set to enabled, which I have now disabled. Have made both those changes, the M.2 SSD is now visible in Disk Management again.

While I was in the BIOS I also noticed that the boot order was:

1. Windows Boot Manager on Disk 0
2. IBA CL Slot 00FE v0010
3. P3: HL-DT-ST DVDRAM GUD0N
4. Intel Volume1

This seemed wrong to me, assuming that Disk 0 is the M.2 SSD, so I swapped items 1 and 4 around, but this resulted in the system refusing to boot. I have now switched them back and it boots once again. This looks a bit like the M.2 SSD has the boot manager but that it is then pointing to the RAID volume for Windows itself. That's not what I want. What would be involved in installing a boot manager on the RAID volume itself so that the system can boot directly to that, and so that I can wipe the M.2 SSD?

I'm afraid it was a fairly boring answer: re-install Windows on the RAID volume. There were a couple of wrinkles, though.

When I formatted the partition that I wanted to install Windows on, then selected it and clicked Next, Windows setup said "We couldn't create a new partition or locate an existing one." I managed to get past this by disabling the M.2 SSD in the BIOS and starting again.

Then at some point a bit further on in the setup it said "Windows could not update the computer's boot configuration." I managed to get past this by deleting all the other partitions on the RAID volume and starting again.

I have subsequently re-enabled the M.2 SSD and removed it from the boot list completely, so I think all is well.