The way it was explained was that Imagine Breaker doesn't negate supernatural events, but returns their balance to them, and as a consequence it makes them into nothing. This is why the Imagine Breaker doesn't negate souls or leylines, since while they may be supernatural, they are in harmony with the world and have their natural place in it. This is also why Othinus wanted to kill him off and made him a target through the previous novels, since he could potentially return the world back to the way it was no matter how far she skewed reality from its original position.
The next novel is likely going to deal with him returning the world back to normal in some fashion. As a side note, it was stated that even if Othinus killed Touma, the Imagine Breaker would simply take form again somewhere else, but its new wielder would take time before they could become a threat.