In modern English, we expect “had changed” rather than “was changed” for this sentence, which probably explains why Oliver Cowdery initially wrote had here. Almost immediately he corrected the had to was (there is no change in the level of ink flow for the supralinear was). The corrected usage here parallels cases found in the book of Daniel in the King James Bible that directly refer to a king’s facial expression:
Book of Mormon usage also supports the use of the be verb rather than have in references to changes in one’s heart, as in Mosiah 5:7: “your hearts are changed” (instead of “your hearts have changed”). Also note the use of was rather than had in 3 Nephi 8:12: “the whole face of the land was changed”.
Summary: Accept Oliver Cowdery’s virtually immediate correction of “had changed” to “was changed”, in accord with both King James and Book of Mormon usage.