The original manuscript has the preposition in (“in whatsoever parts”). When Oliver Cowdery copied the text from 𝓞 into 𝓟, he initially wrote into in 𝓟 (he was probably influenced by the into in the preceding “into all parts of the land”). Somewhat later, probably when proofing against 𝓞, Oliver crossed out the to part of into with heavier ink flow. Nonetheless, the 1830 compositor set into, undoubtedly under the influence (once more) of the preceding into. There are numerous cases in the textual history where into and in have been mixed up, if only momentarily; for a list, see under 1 Nephi 4:33.
There are other passages which support the use of either in or into in the environment of whatsoever and a verb of motion:
Generally in English, the preposition in can occur in contexts involving motion as well as nonmotion (thus “he went in the house” versus “he was in the house”). Here in Helaman 3:5, either preposition is theoretically possible, so we follow the earliest reading, the reading in 𝓞 and the corrected reading in 𝓟. Here is a similar passage where both manuscripts (and all the printed editions) have in rather than into:
Summary: Restore in Helaman 3:5 the preposition in, the earliest reading for the phrase “in whatsoever parts it had not been rendered desolate”.