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There are two drives in the machine:
m.2 slotted into the mobo directly
"normal" form factor SSD that's plugged in via SATA cablesThe "new" m.2 is loading Windows now as a newly formatted boot drive and the data drive, that was accessible via USB Windows Repair media is now gone. I'm jiggling cables now and going to try again before I set fire to everything.
hippy-
Is the 'new' M.2 form factor drive a SATA or NVME interface? Both are possible with the same form factor. Some motherboards dynamically re-allocate PCIe lanes and enable/disable ports when you plug stuff in; sounds like this is happening.
Have you checked the SATA port settings in the BIOS to make sure they're all enabled? Have you manually installed the correct chipset drivers in Windows?
ectoplasmosis
Is the non-detected M.2 in a slot that's routed via the chipset? It could be down to dynamic PCIe lane allocation, and correct chipset drivers being required to re-allocate lanes and enable the slot...