NOTE: I have solved my question before publishing it. I have since written a guide for myself. As the question and the answer were already written and I didn't find any post on SO dealing with this specific issue I thought publishing it and sharing the solution would not cost much and maybe help some people :)
Question
The context I have is that I am saving configuration files on my system in a git repo. Some time ago in the repo I added someconf.conf file, and since then I have modified it in multiple commits. In the future I realize this file was automatically generated by the system at first and then I started modifying it. Thus the first commit comporting someconf.conf (let's call it A1) will have the {initial system config} + {modif1} and the subsequent commits will have {modif N} (let's call them AN) each.
So now I want to be able to create a commit B1 that would be the new one to originally add someconf.conf in my repo and only include {initial system config} then the A1 would be transformed into A1' that would now only include {modif1} compared to B1 and thus the new history would be ...,B1,A1',...,A2',...A3'
I managed to do it like so