And he kept his "new" training methods separate from the Aikido classes he was teaching (in the kenkyukai). If I'm not mistaken, his new training methods were also one of the sources of friction that led to the split...
If my understanding of the timeline is correct, he did not initially separate his "new" training methods, however, once the friction had arisen, he agreed to do so in an (ultimately unsuccessful) attempt to smooth things out.
If my understanding of the circumstances is correct, while great public emphasis is placed on differences in philosophical and methodological approach, we are talking about a family business, and it would be remarkable if rather more private familial issues didn't also played a role.
After all, Ueshiba K. and Tohei K. were married to sisters.
This makes the current heads of Aikikai Hombu and Ki no Kenkyukai first cousins, if I'm not mistaken.