did you put windows onto the new ssd or is it just storage? If you put win 10 on it, it might answer mystery but only if the 128gb ssd wasn't in PC when you installed on other.
just to be different, the boot order doesn't appear to show on the boot tab -
https://dlcdnets.asus.com/pub/ASUS/...FX_R2.0/E8042_SABERTOOTH_990FX_R20_V2_WEB.pdf - can you show me a screenshot?
Windows can't change boot order so what is showing as 1st if the 2nd ssd is attached as if its blank, it shouldn't override the ssd that was already in boot order. It shouldn't do anything to boot order at all.
I can see references to legacy but no where it mentions how to swap boot method from Legacy to Uefi - that could be reason it can't see normal drive if its swapped the boot method (this only happen if you put win 10 on new ssd)
its not because secure boot is on as motherboard doesn't have secure boot.
with only 2 partitions on the 128gb ssd, I can tell its formatted as MBR so if the boot method has swapped to UEFI, it might be looking at ssd 1st