In theory, the clause headed by notwithstanding here in Helaman 12:6 could belong either to the preceding text or to the following. The 1830 compositor set the punctuation so that the clause was attached to the preceding text (he placed a semicolon after the clause), while the editors for the 1920 LDS edition moved the semicolon to before the clause, thus attaching the clause to the following text. The 1953 RLDS edition placed a semicolon before the notwithstanding yet left the one after the clause, thus totally isolating that clause from its surrounding text.
In this passage there is a natural connection between God’s goodness and mercy, on the one hand, and his desire to counsel and guide his people, on the other hand. In other words, there is an appropriate connection between the notwithstanding-clause and the following text. The decision in the 1920 LDS edition to associate the notwithstanding-clause with the following text is the more natural reading and will be followed in the critical text. See under Alma 17:15 for discussion of other notwithstanding-clauses for which there has been some confusion over whether the clause should be associated with the preceding or the following text.
Summary: Maintain in Helaman 12:6 the punctuation introduced in the 1920 LDS edition; the notwithstanding-clause associates more appropriately with the following text.