“the innocent blood that he had shed.” This is also mentioned in 2 Kings 21:16.

“and Yahweh was not willing to forgive.” God will forgive sin if people truly repent and confess, so this verse is not saying that God will not forgive the killing of innocent people. History is full of murderers who God has forgiven, including the apostle Paul. What this verse is saying is that the sins of Manasseh were still affecting the people of Judah over 30 years after Manasseh died, and so because of the ongoing sin God could not forgive Judah. By the time of 2 Kings 24:4, during the reign of Jehoiakim, it had been over 30 years since Manasseh died, and those 30 years included Josiah’s reform during which the Temple was repaired and the feasts kept. But as good and godly as Josiah tried to be, he never cleansed Judah of its deeply-rooted sin. What was really going on such that God could not forgive Judah was happening both in the spiritual and the physical realm.

On the physical level, people who had participated in the terrible sins of Manasseh were still around and still affecting Judah. Some of those people were likely in the royal family, some were likely high officials in the kingdom, and some were likely high-ranking military officers. These people would still be doing evil, even if it was not being done on a national level or very openly. On a spiritual level, the heinous sin opened the door for demons to infiltrate the kingdom and influence people’s thoughts and actions, as well as cause other types of disasters such as famines, floods, destructive weather, etc. When demons are empowered by sin to work in a family or kingdom, they work to get deeply rooted in it, and therefore do not leave just because a righteous ruler comes to power. It takes years and diligent work to clean a kingdom or family of the influence of demons, and stopping egregious sins such as murder and idolatry—and there are other such sins as well—is part of cleansing the kingdom in the sight of God.

The fact that a kingdom or nation can be adversely affected by sin and evil long after the primary sinner or sinners are gone is the same reason that God says in the Ten Commandments that if people are involved in idolatry that they will suffer the consequences of that idolatry to the third and fourth generation (Exod. 20:5). Although some idolatry is simply the result of ignorance, a lot of idolatry reveals the disdain and defiance that a person has for God, and that attitude is usually passed down in whole or in part from parents to children. Furthermore, the idolatry also allows demons to come into the family in various ways, including demon possession and oppression, and also direct demonic influences that cause destruction, sickness, and poverty.

The world is a war zone between Good and Evil, and when we humans are evil, God cannot protect us from the evil spirits that we allow into our lives through our ungodly behavior. Also, sadly, as in any war, there is collateral damage, and other people who are doing their best to be godly often get hurt.