Isaiah 49:21 (King James Bible) behold I was left alone these / where had they been
The ink level for the correction from had to have in 𝓞 is the same as that of the original hand; thus the correction seems to have been an immediate one. The phraseology of “where had they been” is rather awkward. While it is true that one could interpret the change as Joseph Smith’s decision (while translating) to replace the awkward had with have, it is also possible that the pasttense form had was actually a scribal error influenced by the preceding past-tense form was. Since the correction appears to be immediate, it is probably best to accept the correction have as the reading of the original text for the Book of Mormon, even though it disagrees with the had of the King James Bible.
Either had or have would work in a translation from the Hebrew, since the Hebrew text here has no actual word for the be verb (which is why had been is in italics in the King James text). Another possible translation could have been “these / where were they”.
Summary: Maintain in 1 Nephi 21:21 the have of “where have they been”; the correction in 𝓞 from the had to have appears to have been immediate; the initial had is probably due to scribal error, even though it does agree with the had of the King James Bible.