I only have one NVMe drive installed, 970 EVO boot drive in M2_1 slot of X470-F, and between BIOS and Windows 10 running have only seen mention of PCI interface used for the drive in Samsung Magician software. When selecting any drive installed on the PC Magician shows the interface and shows "PCIE Gen. 3 x 4" for the 970 EVO and "SATA 6.0GB/s" for all other drives. Maybe it would show PCIE Gen. 3 x 2 for the M2_2 drive if an NVMe was installed there? Disk Management, which appears when first installing Windows 10 to allocate boot drive space, did not show any unique identifier of PCIE slot even when choosing properties>details location information. The Location Information for my 970 EVO and 850 EVO are the same, Bus Number 0, Target Id 0, LUN 0, while my other drives all have unique Bus Numbers associated.
I'd remove M2_2 drive, install OS on M2_1 and reinstall M2_2. Not having access to the physical PC is a whole different issue I'll stay away from.
X470-F, 2700X, 5700 XT Nitro+, 970 EVO, LanCool 2 Mesh Performance, H115i Pro, 16GB3000C14, TT650W Gold