Three of the Book of Mormon scribes (Oliver Cowdery and the two unknown scribes in 𝓞) often spelled the conjunction than as then, probably because they pronounced than like then. This reduced pronunciation for than has been very common in dialects of English, including American ones. These three Book of Mormon scribes also frequently spelled than correctly. Hyrum Smith and the unknown scribe 2 of 𝓟 virtually always spelled the conjunction as than. Presumably the original text distinguished between the conjunction than and the adverb then. In the current text, the spelling is correct for every example of than and then. For a complete discussion, see than in volume 3.
Historically, the lexically distinct than and then derive from the same Old English adverb (see under than in the Oxford English Dictionary), and in many Middle English and Early Modern English texts then is consistently used for both than and then. And even in standard English today, both than and then are identically pronounced with a schwa vowel in unstressed contexts.
Summary: The scribes often spelled the conjunction than like the adverbial then; the original text apparently distinguished between the two words, so we make the standard distinction between them in the critical text, allowing the context to determine which one is intended.