Chapter 1290: The Impossible Might Be Possible.

You can overwhelm each small piece of the soul fragment individually after cutting them up instead of struggling with the whole soul fragment. That will increase the chance of success of the brainwashing and avoid memory backlash which causes reverse brainwashing. 

Even if reverse brainwashing doesn't occur, there can be some other complications during the process. The soul might become aware during the brainwashing and resist. That is unlikely if you made sure to cut it up into a small enough piece. 

Legion-5 was meticulous with his cuts so these pieces didn't wake up. If they did, then he would crush their resistance with the soul blade. Chop them up and brainwash their smaller pieces individually all over again.