If you miss a single collectible, you do not need to replay the entire game. Find a save that is at 99% completion, note which collectible is missing, load that mission, grab it, and the trophy will pop immediately.
Beyond mission progress, saves your profile data separately. This includes your character rank, unlocked weapons, camouflage skins, and multiplayer stats. This data is stored locally and syncs with the cloud (if playing on Steam or consoles), meaning if you start a new mission but your rank hasn't updated, the profile save hasn't triggered yet. sniper elite 4 save game