If the reason for the differences was done intentionally in Lean (as opposed to hallucinate e.g. m+4 vs m+5 as mentioned in remark 3.2), then a simple recording of differences, and then afterwards pass back any changes to the original NL would fix the issue. If it was hallucinated, then there is no guarantee it wouldn't keep hallucinating, and thus you might never end up with the same proof no matter how many passes you do back and forth (see remark 3.4).
"Incomplete" proofs might be a way of viewing this. You have a NL argument to prove X. It turns out the NL proof has holes you can drive a truck through. So... you go around and patch the holes.
The resulting proof is different! You can start off with a bad proof and find a correct proof. Sometimes.
EDIT: for French speakers (maybe autodub gets you there) I saw a very nice simple case of this recently. A commonly stated proof for a relatively simple theory. The proof has a giant hole in it, and completing it requires some work [0])
humans as a whole have always known the weakness of natural language is in its precision. In a way this isn't strange that this issue has come up.
> The agents arrived at their resolution on Saturday, September 5, about 88 hours after the first agents were launched. Lean formalization and verification took an additional 17 hours via GPT‑6 Astra.
This seems pretty clear that they found the proof first and then mechanized it afterwards.