I've run into this with source code archeology projects. Git is ill-suited to integrating newly discovered pre-history/missing intermediary history steps. Any new historical change, out of necessity, alters all subsequent commit hashes. This means collaboration and permalinks can't happen like with "normal" Git repos.
Does anyone know of any tooling or an alternate vcs which has the ability to integrate new pre-history or alternate history (e.g. original branch commits alongside a squash and merge commit) without requiring completely breaking/re-writing the entire tree?