However the Agents while they didn't change the "past" of the individual characters who went through the loop they did know of the "past" of all of humanity that didn't make it to the lighthouse and they changed that "past", having lived in the future, as they were in a historian from the future travelling back to save them.
So while in Infinity War/Endgame the snapture still happens, with people supernaturally brought back to life in AoS the Graviton crack of the earth no longer happens. People are not brought back to life, they are never killed in the first place in the last loop of time changing the past.
For the Chronocoms, while the survivors may retain knowledge of what happened in their past like the agents did, they are not looking to bring back the Shrike dead but to prevent a Shrike victory, changing the past of the greater community, in the first place. Just as Quake did, changing the past by finally beating Graviton when she used the serum meant to save Coulson's life.