Note: I don't know what the comments were - partial answer or request for clarification.
In that type of situation, I would usually go with option 3...
- say something along the lines of "thank you for pointing that out, I've removed my comment and written a more complete answer - feel free to tidy up this thread; I'll tidy this & other comments after giving you chance to read this.", notifying the author, and allowing them to remove their comment.
Whether or not that reaches the desired effect, I would flag it for myself [actually keep the tab open on a separate window] & come back to it up to 24 hours later [depending on how active the original conversation was] to tidy up my own comments.
At that point, any remaining comments that are no longer useful or relevant I would flag for a mod to tidy.
I'd also note that some stacks are much more aggressive/diligent at comment thread tidy-ups than others, so some of the above can depend on the stack.