I will try it again with stable version to confirm about this. I hope somebody else can test it and reproduce my experience, because I am afraid that this is only my subjective personal perception as examining many enemies in one screen that enter and exit the screen in a fast battle scene is little bit tricky. In the current condition, I can still finish a chapter without problem, because I can defeat enemy officers without interrupted with random disappearance even though other enemies onscreen that not engaged in battle with my character still randomly appear and disappear.
I am not sure it is the expected behaviour in real PSP or it is by design to free up memory. Now in PPSSPP latest build, the enemies that I still attacking or enemies in the center of screen don't randomly disappear, but enemies in the corner of screen that looks not important still randomly appear and disappear. Previously, most enemies or allies will randomly disappear even though I don't do any action. But I can still see other enemies randomly disappear.
The result is the annoying bug when enemy officers suddenly disappear when I was attacking him is gone. Warriors Orochi 2 is set right after the first game and once again you are trying to defeat the big evil Orochi and that is. I have tested the last build without disabling any JIT options.