Or the AI wrote a NL proof of Navier-Stokes, began rewrite in Lean, then discovered a false / handwavy / easier to write in Lean / etc approach of some parts of the proof, and modified it accordingly. Since there wasn't any backpass from Lean to NL to include any changes it did due to any of the above reasons, the proofs aren't identical. That's what I think is most likely.

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).