Samuel has just related the terrible destructive forces that will be unleashed at the time of Christ’s death. The question about those destructions was not whether or not they would come, but how they would affect these Nephites. Samuel tells them that it depends upon their repentance. If they do not repent, “[their] houses shall be left unto [them] desolate.” While the destructions certainly open the possibility that Samuel was threatening a dwelling place, it is also possible that he was speaking of the lives of the people and their families. The house was both a physical structure and a metaphor for the people who lived there, and that included descendants.
That it was the destruction of people becomes evident in verse 2, which deals with the plights of women and children. Those most vulnerable inhabitants of the land “shall have great cause to mourn.” They “attempt to flee and there shall be no place for refuge.”
In verse 4, Samuel specifically mentions the people of Nephi twice. That sets up the next verse where Samuel will contrast them with the Lamanites.
Samuel notes that the Nephites “have been a chosen people of the Lord.” They will lose that status if they do not repent.