How long do Japan keep foreigner information?

I plan to naturalize to get a Japanese passport. However, my concern is when my parents used to be in Japan, the head of the household was registered as my father. After, he returned back to his country he changed his name legally, and my father's name in my current citizenship is different from one that was previously registered in Japan. Will Japan be able to figure it out cause it may cause some problems during the application process due to different father names. Additionally, I was born in Japan.

Also, due to some reason he cannot provide me the proof of a change in name.

did you try contacting the embassy?