It is probable that during the reign of Queen Athaliah, who worshiped the false god Baal, that the high priest of Jerusalem knew of Athaliah’s evil intentions to destroy the temple of God and cease its religious objects. So, he and the priests hid the Ark of the covenant to protect it from this evil queen.
And in order to hide their deed, the priests continued their worship services as if nothing had happened. The high priest entered the Holy of Holies, and he was silent about the disappearance of the Ark and he sprinkled the blood of sacrifice before the Lord in the Holy of Holies. Thus, the sacrificial rituals continued as before, but without the presence of the Ark in Second Temple (Mishnh Yoma5:2).
It is true that God’s presence dwelt between the two cherubims over the mercy seat (Exodus 25:17-22), where the blood was sprinkled by the High priest (Exodus 25:17-22), but God’s presence was not only limited to the existence of the Ark in the temple. And when Jehoash captured the temple in 786 BC, he too acted wisely by not mentioning the Ark’s disappearance, to avoid religious consequences.
This secret continued until the time of Jeremiah who declared: “men shall no longer speak of the Ark of the Covenant, nor shall it come to mind. They shall not mention it, or miss it, or make another” (Jer. 3:16). Jeremiah predicted the coming of the time when God would set up His abode upon the earth. God’s actual presence would make the symbol of His presence superseded.
Jeremiah‘s declaration that no Ark would be made in the future suggests that being a prophet belonging to the priestly line, he knew the secrets of the temple and that the Ark was no longer in existence.
The temple in Jerusalem was captured first by the Babylonians (Nebuchadnezzar) in 597, 586 BCE, and then later by the Romans in 70 AD. Thus, the Ark was preserved from these enemies for it contained the only document on Earth that was ever written by the very finger of God – the Ten Commandments (Deuteronomy 10:4, 5).
In His service,
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