If a 3k user votes to close a question A as a dupe of B and then another user dupehammers to C, both B and C are listed in the close notice.
However, when a user with <3k rep flags as a duplicate of B, and then A is dupehammered to C, it's only closed as a duplicate of C. IMHO the former behaviour is desired for flags as well. The problem is compounded by the autogenerated flag comment being deleted when the question is dupehammered, so that a potentially useful comment is lost to the OP.
Thankfully, the linked questions list still includes question B.
Note that this is only about dupehammered closures, where the list of questions can be edited by the hammer-wielder. So, they can edit in B if they find it useful, but IMHO it should be the other way around: B should be included by default and edited out if necessary. I think B may likely be of some use to the OP, so removing all obvious links to it but keeping it in the sidebar is a bad move.
An example: https://askubuntu.com/posts/998931/timeline