According to the following lines in the output:

sky130_fd_pr__diode_pw2nd_05v5 (1)         |(no matching element)
(no matching element)                      |sky130_fd_pr__diode_pw2nd (1)

The problem appears to be a difference between the diode model name. I need to figure out what source was at fault. I recall fixing this in the magic techfile in open_pdks recently, which is probably at the root of the problem. How was the 2nd netlist generated?