Here we have a clear example of where Oliver Cowdery mistakenly wrote whether in place of the correct whither —namely, in 𝓟, when he copied the text from 𝓞 (which is extant here and reads whither). As explained under 1 Nephi 22:4, Oliver tended to mix up the spelling of these two words. Here in Alma 63:8 the text is referring to where the other ship went, not whether she went.
Summary: Maintain in Alma 63:8 the use of whither in “and whither she did go we know not”.