So Isshin told Ichigo his engetsu didn't want him to learn the final getsuga, so does that mean that he has used it before? Otherwise how else would he know that there was a final getsuga?
So lets assume that he did use it, then how did he get his powers back?
1. Maybe he had something to do with full bringers
2. He couldve had shinigami transfer powers to him as they did with ichigo.
Him losing his powers may explain how masaki died. I mean if he had lost his powers during this time he wouldnt have been able to prevent it.