Here we have an example where the and those have been mixed up in the early transmission of the text. The original manuscript may have read either “those cities which had been taken by the Lamanites” or “the cities which had been taken by the Lamanites”. 𝓞 is highly fragmented near the end of the line, and it is difficult to tell if the line ends with tho or the. If tho, then presumably a hyphenated se should be found at the beginning of the next line. But the first couple of words at the beginning of the next line are not extant. Spacing in the lacuna favors the slightly longer “-se cities which”, but “cities which” would also fit.
When Oliver Cowdery copied this passage into the printer’s manuscript, he initially wrote “the cities which had been taken by the Lamanites”; later, with a slightly sharper quill, he overwrote the e of the the with an o and then supralinearly inserted se. The ink appears to be slightly blacker than the original ink, implying that this correction was made later—at about the same time the correct himself in verse 16 was changed in 𝓟 to themselves on the preceding page of 𝓟 (see the earlier discussion under Alma 58:16–17). In any event, the correction here in verse 31 was definitely not immediate. All the printed editions have continued with the corrected reading in 𝓟, “those cities which had been taken by the Lamanites”.
Elsewhere in the text, we can find evidence for both those and the in this context. For instance, there are four occurrences of “the cities which” and five others of “those cities which”. This variation suggests that there wouldn’t have been any tendency for Oliver Cowdery to consciously edit the to those in Alma 58:31. Therefore, the corrected reading in 𝓟 is most likely a correction to the reading of 𝓞. When Oliver copied the text into 𝓟, he may have misread the line-final tho as the. See under Alma 11:21 for other cases in copying from 𝓞 into 𝓟 where Oliver misread words at the ends of lines in 𝓞.
In a similar example earlier in the book of Alma, Oliver Cowdery initially replaced an original those (extant in 𝓞) with the in 𝓟. In that case, his correction in 𝓟 was virtually immediate (there is no change in the level of ink flow); he overwrote the e with an o and inserted the se inline:
For another example where those was replaced by the, see under Alma 63:10. There the 1830 compositor mis-set “those people which had gone forth into that land” as “the people which had gone forth into that land”.
Summary: Maintain those in Alma 58:31, the corrected reading in 𝓟 and the probable reading in 𝓞: “those cities which had been taken by the Lamanites”.