I tried deleting the params file and still got the same result of two external mags. Are you able to replicate this error on your hardware?
I did a test where I calibrated the mag with v1.5.4 and then loaded the params using v1.6.0 and both the internal an external mags appeared. I then calibrated a second time with v1.6.0 the internal mag was replaced with duplicate external mag values. This looks like a bug in v1.6.0 calibration routing for the snapdragon flight.