When using the PCIe to SATA or PCIe to USB, you must flash the 2PCIe-1Lane firmware image, since mPCIe A/B lanes have two configuration options: a single 2-lane interface(mPCIe A) or two separate 1-lane interfaces(mPCIe A+mPCIe B).
Enter the commands: lspci and cat /proc/partitions . These can be used to check SATA and all block devices currently recognized by the Linux kernel, along with their primary information.
Afaik pcie on mPCI slots r4lite is only selected by gpio (GPIO11) and in code i saw 2 overlays (only define this gpio as gpiohog with low/high setting)…does it really flashing new image?
Not sure how the overlays are loaded in bpi image but if you can select them somehow or drop (to set gpio11 in uboot manually and linux does not change it) it should not require reflash.