ImagineBreaker

I probably didn't put that sentence together correctly. He lost the skills he had gained over two erased years. The skills he had gained before that were still with him.

Makoto entered the academy as "Ultimate Lucky," and he didn't get "Ultimate Hope" until late in the game.

Perhaps the sentence was misspelled. What was meant was that in 19 years, memories like Junko's name and what she looked like were erased. Only two years were completely erased, and those two years included the skills he learned during that time.

That was the plan.

It's not a big deal. The system has nothing to do with it. It's just that the thing that wiped the memory was created by Yasuke, that is, with the help of the system. The system doesn't force the canon either, there are no penalties. It's just that these two options, were the only ones available. Roughly speaking, either leave or stay (and no matter what happens in between). Options such as kill yourself or become executed, I thought it was not logical to add.

He lost skills in two years, not the whole time. Chihro (Programmer) was involved in AI, even before he entered the academy. So he could make one.

Something like.

She was a noreal in canon, too. The world just looked different to her.

You know... I agree. But without the killer game, there just wouldn't have been any point in starting the story. Plus Junko "Ultimate Analyst" she could have come up with something.

The memory is in the body of the protagonist, and the skills are in the system. But they were also deleted and the system... well, roughly speaking, offers to unload them from the cloud.