The original manuscript is not extant here, but spacing between extant fragments clearly supports the longer the Lord. Oliver Cowdery accidentally wrote he initially in the printer’s manuscript, but then virtually immediately he corrected the he to the Lord (there is no change in the level of ink flow). He may have been influenced by the two following instances of he in this sentence (“that he had delivered them from death … and he had delivered them out of the hands of their enemies”). Elsewhere the text usually has the full subject, the Lord, in this expression (there are five instances of “how great things the Lord hath/ had done for X”). But there is one instance where we get the pronoun he: “how great things he hath done for them” (Mosiah 27:16). In each case, we therefore follow the earliest textual evidence; here in Alma 62:50, we follow the corrected reading in 𝓟, “how great things the Lord had done for them”.
Summary: Follow in Alma 62:50 the corrected reading in 𝓟, “how great things the Lord had done for them”; spacing between extant fragments of 𝓞 supports the Lord rather than the pronoun he.