When I was testing it with numbers as you did, it seams to work, but then I replied on some older comment, as soon as I refreshed the page my reply went down. See attachment.
Also in terms of the design, it would be nice if we could see it more clear that it is reply on the comment. Kind of like Facebook does. Shift it to the right or something. Our previous theme did it too. Because now it is all the same and you don’t know who replied on what.
