Here the 1830 typesetter interpreted after that as a prepositional phrase (thus he placed a comma after the that). Using a semicolon, he also separated off the main clause at the end of the verse (“therefore I am commanded that I should hide them up again in the earth”). The editors for the 1920 LDS edition further broke up the sentence by placing a semicolon after “they have all dwindled in unbelief”.
Within the larger passage, there are actually four instances of the subordinate conjunction after:
In this passage there has been some variety in how the after has been treated. In the editing for the 1837 edition, the original that was removed after the third instance of after (in verse 2), but not after the first instance (in verse 1). Interestingly, the second instance of after (at the end of verse 1) lacked the that in the earliest extant text, so there was no that there to be removed in the editing for the 1837 edition. Of course, the that after the fourth after was not deleted since the 1830 typesetter had placed a comma after the that.
Under Alma 5:5, I list four cases in the original text of actual prepositional after that. In all those cases, there is a clear notion of a sequence of contemporary events (‘X happens; and after that, Y happens’). But here at the beginning of Ether 4, there is no such attempt to delineate a sequence of contemporary events—in fact, several hundred years elapsed between the time Christ commanded that the record of the brother of Jared “should be made manifest” and the time Moroni hid up that record. Here at the beginning of Ether 4, Moroni is explaining that the words in the brother of Jared’s record were originally kept from the Nephites and Lamanites until the Savior visited them, but now that the descendants of these people have apostatized, Moroni has been commanded to hide up these words once more. This interpretation of the larger passage works much better than the current text with its comma after the that in verse 3.
It should also be noted that this interpretation of the fourth after as a subordinate conjunction leads to a striking structural parallelism between verses 2 and 3:
This parallelism even extends to the pronominal references for the third person plural pronoun: in the A/Aªparallel, they refers to ‘his people’; in the B/Bªparallel, they /them refers to ‘the words of the brother of Jared’.
In the larger passage, the critical text will restore the original that after the third after and maintain the two other cases of after that (the first and fourth ones) while leaving the second one without any that. And in verse 3 the comma after the that and the two semicolons will be removed so that the fourth after- clause will be completed by the therefore- clause:
Note that the independent clause preceding the final therefore-clause is treated parenthetically.
Summary: Maintain in Ether 4:3 the that that follows after, but remove the following comma since what we have here is a subordinate after- clause; also remove the two semicolons in this verse so that the after- clause will be completed by the therefore- clause; also restore the original instance of after that in verse 2.