The 1874 RLDS edition accidentally omitted the first had in this sentence. It was restored to the RLDS text in 1908. Parallelism with the following conjoined predicate (“and had obtained possession of the city Mulek”) provides support for the first had. For most instances of a conjoined past-perfect predicate, the preceding predicate also has a past-perfect had (as here in Alma 53:6). But there are instances where the first predicate lacks the past perfect auxiliary, as in Alma 1:19: “those that did belong to the church of God and had taken upon them the name of Christ”. In each case, we follow the earliest textual sources, thus the had in both predicates for Alma 53:6.
Summary: Maintain the use of had in both conjoined predicates in Alma 53:6: “Moroni had thus gained a victory … and had obtained possession of the city Mulek”.