I dated a Japanese girl for 4 years throughout college. We spent basically every moment of every day together and then she just disappeared. Haven't heard from her in 11 years now.
Did you go to school in Japan?
If not, then did it not occur to you that a Japanese student studying abroad would need either a work permit or a marriage visa to stay?
She probably was expecting you to propose and since you didn't she left because she had to.
I went to school in the US and she is not actually from Japan. Both her parents were from Japan though despite her being born in the US. It could be a coincidence and have nothing to do with this Japanese cultural phenomenon, but it seemed pretty relevant to what I experience.