𝓞 is extant here and reads “save it were those parts which had”. When Oliver Cowdery copied from 𝓞 into 𝓟, he momentarily inserted an expletive it in the relative clause: “which it had been commanded by Alma should not go forth”. Virtually immediately Oliver caught his error and crossed out the extra it (there is no change in the level of ink flow for the crossout). His error was probably prompted by the preceding it in “save it were those parts”.
There are instances of original expletive it that have been removed from the text. For some examples, see the discussion under Alma 43:46. The critical text will retain all original instances of expletive it, but not the one that momentarily entered the text here in Alma 63:12.
Summary: Maintain the original reading in Alma 63:12 without any expletive it in the phrase “those parts which had been commanded by Alma should not go forth”.