Spoiler referente à 2ª temporada:
The hatred and bitterness that Henry is showing in the scene you mentioned earlier is - at least that's what I'm getting from it - supposed to be directed at Beverly Barlowe. In later scenes, Henry's angry words "I will never forget." are shown in flashbacks, when the topic of Beverly causing Kim's death comes up.
Spoiler sobre as temporadas 4 + 5:
In the new timeline, Henry gets to know Grace and at least at this point in time he is over the loss of Kim (Although one could argue that the bio-computer-thingy from season 3 had already given him closure).
Para concluir: Não, eu não acho que algo tenha mexido com o passado / memória de Henry. É que Jack nunca foi o verdadeiro destinatário da hostilidade de Henry. (Embora os escritores possam ter deliberadamente implicado isso em cenas anteriores)