One tier would be the email archive, containing all discussions. Links to the original entries would be automatically maintained. When posted to the mailing list, they would become part of the archive, with the ability to collect responses. Copying the email version from the email archive into the document archive might then take all of the responses it had collected along with it, where further edits could occur. This is a key issue, especially in a hierarchical system.
Nodes can change position, have contents changed, or be deleted.
One part of the solution is node IDs. That takes care of nodes that move to a new position. Performance is still an issue, but those concerns are probably addressable with a good design. Another part of the solution may be two-way links. The problem with invalid links, after all, is that they look fine until you traverse them.