This has been on our list to fix since https://news.ycombinator.com/item?id=10917057 so I went ahead and fixed it (or tried to). Now, in addition to "[flagged]", "[dead]", or "[deleted]", you'll see the usual item line with at least a timestamp. Hopefully this will make it clear that there used to be a full comment there, to which there is a surviving reply.
You can turn on showdead in your profile to see comments that have been hidden.
It was displayed as if it was a reply to mine - in place of the deleted comment there was just "[flagged]", but no date or anything, so it looked like a tag added to mine. This isn't most readable UI...
Thanks for the showdead tip.