The original text here has three occurrences of the subordinate conjunction that. The last one (“that he should not partake of the fruit”) heads a resultive clause. But the first two that-clauses are conjoined complements and act together as the direct object for the verb see; skipping the intervening subordinate lest-clause in this passage, the text reads as follows:
now we see that the man had became as God / knowing good and evil and … that the Lord God placed cherubims and the flaming sword …
The deletion of the second that was probably intended since its inclusion leads to a difficult reading when preceded by the lest-clause. Nonetheless, in his editing for the 1837 edition, Joseph Smith did not cross out this that in 𝓟. The critical text will restore the second that in Alma 42:3.
Summary: Restore the original second that in Alma 42:3; the that-clause here serves conjunctively as part of the direct object for the main verb see at the beginning of the sentence.