The larger passage here consists of several different types of editing, all initiated by Joseph Smith in an attempt to smooth out the text. This editing represents Joseph’s early attempts to clarify the text, but this kind of editing soon ceased since it was probably time-consuming and not really necessary. We first consider Joseph Smith’s editing of the subordinate conjunctive phrase “how that”.
His editing here seems to be motivated by an attempt to deal with the complexity of the subordinate clause (“after they were destroyed”) that follows right after the “how that”. Later on in the book of Ether, Joseph edited out a similar example of how; in this case, the following clause (“after the waters had receded from off the face of this land”) is also subordinate:
But in five cases, the phrase “how that” has been retained; in each of these cases there is no following subordinate clause after the “how that”:
In any event, there is no crucial need to delete the how from 1 Nephi 10:3 and Ether 13:2, despite the increased complexity of having an after-clause immediately follow “how that”.
Summary: Restore the original connective “how that” in 1 Nephi 10:3 and Ether 13:2.