In the second half of this passage, the narrative starts over with a repetition. The earlier when- clause, under 1, is very long and is never completed, so basically Moroni starts over at the end of his first when- clause and summarizes what he has just said, under 2 (“and it came to pass that when they had done all these things”). The LDS text has allowed this difficult construction to remain in the text, but the 1953 RLDS edition changed the first subordinate when- clause to a main clause by deleting the when (the past-perfect auxiliary had was also removed).
Elsewhere the original text allows for incomplete subordinate clauses. See, for instance, the discussion regarding the incomplete present-participial clause in Enos 1:1–2 (discussed under Enos 1:3). The critical text will maintain the original reading here in Ether 6:4.
Summary: Maintain the incomplete when- clause in Ether 6:4; although unacceptable in the writing style for modern English, such usage does occur in the original text of the Book of Mormon.