PKHeX is built to support unmodified game save files. PKHeX cannot know what changes you've made to the ROM.
Since you are playing a ROM hack, the modifications by the patcher likely changed more than just bypassing trade evolutions. It probably mirrored ability slots (wrong, a single-ability species needs XX-00 not XX-XX).
Changing the ability selection will cause the program to recalculate a PID, hence the second image.
Copy the PID, then fix the ability index, then paste the original PID back.