So, long story short, if The character's ID/Handedness is 00 at the start of a battle (As inactive characters' will be during an autobattle), the game skips copying their basic critical hit percentage (7E:202D,x) into their effective critical hit percentage (7E:2041,x). The number at 2041 gets copied back to 202D, which gets copied back to 102D regardless at the end of the battle. So if 2041 is never changed from zero, then that zero gets copied into the permanent character record. So, within the instructions of how to handle a blanked-out character, there is a JMP instruction that jumps right past what we want:
$03/94E7 4C 70 95 JMP $9570 [$03:9570]
What we want to do is jump to the point where that value is copied
into 2041, so we just change the "70" at 394E8 to a "23." The end result is this:
$03/94E7 4C 23 95 JMP $9523 [$00:9523]
Anyway, that will fix our issue with inactive characters losing their critical.
In regular ROM (unheadered), this change will be at 01/94E8.