As for what happened in the end, he was trying to perform a delicate procedure on her of manually rewriting memories (more difficult than just giving orders or the various automatic procedures) and due to the emotional duress of doing it to mia specifically triggered his levelup to level 2 midway through. Causing him to go out of control and give her brain damage.
You give him too much credit.
He just wanted to suppress all memories of Ella.
It's the same as suppressing everyone else's memories that he was fat.
But it has been said several times that Mia is extremely intelligent (genius), had a strong will, and was aware of exactly what he was doing to her. As a result, her resistance was much greater, forcing Jake to use much more power, which brought him to the limits of his abilities. If you remember, Ella later told him (in hospital) that if he tried something like that on superhuman or a monster, it could kill him. This is also the reason why all his commands are subtle and he does not try to get people to do things that no one will could force them to do.
Relatively similar things apply to real-world hypnosis.
You can make a man bark like a dog, but you can't make him take a knife and cut his neck.
Your subconscious protects you from things you would never do.
