I think I have a good explaination that came from Sapphire's mouth herself.

The episode Keystone Motel to be exact. Sapphire comments that she usually looks at the endgame when it comes to the future. She saw Garnet eventually reconciling with Pearl, ergo that's all she needed to know. Everything in between was just fluff and if the course was stayed everything would go as she sees. So if she looks into the future and sees a healthy adult Steven, then she doesn't need to worry about what comes in between.

So in this instance when they say she doesn't know what to do. She means it. Garnet saw the future and saw a healthy adult Steven. This does not mean that she knows how they will get to that conclusion