Lobste.rs has what they call "merged stories", where the moderator will merge into a single page the links for a few submissions, as well as the comments from all submissions. Here's a recent example: https://lobste.rs/s/djejmh/really_really_good_random_number
I guess it's similar to what you do here when you "move" comments from one submission to another. A downside is that it can be hard to know which comments come from which submission. Perhaps top-level comments need a small marker indicating which link they originally commented under?
Comments from merged stories do have a label showing where the came from... but only before the merge; afterwards top-level comments are always attached to the primary story which is when things get especially confusing.
If anyone is real curious about the fine details, I've done almost all of this feature work on Lobsters office hours streams: https://push.cx/tags#story-merging I plan to continue that work in about four hours on today's stream so it's a great time to ask questions: https://push.cx/stream
As a (much) smaller community, story merging has been valuable for allowing us to build the critical mass of a good discussion. We also avoid rehashing the basics/easy misunderstandings. It's a pretty similar to dang's motivation about wanting to promote novel discussions. I have joked for a couple years that I'd love to see HN copy the feature so that HN can teach everyone how the feature works.