Continuing his account of the end times, Nephi notes that while there is a war between the abominable church and the church of Jehovah, Jehovah will be victorious. The wicked will not destroy the righteous. This is the ultimate promise Jehovah has made to his people, but it does not preclude the times when the righteous will suffer before that final day. Those times are also predicted.
In the prophetic vocabulary, “these things must shortly come” clearly does not mean what a plain interpretation would mean. The idea that they would “shortly come” is a call to current preparation, not the timing of the final events. The majority of humanity will need to be personally prepared to meet their God long before God initiates the final days.