The Ark was placed on a stone in the western portion of the Holy of Holies. The vial of manna and Aharon's staff were placed before it.
When Solomon built the Temple, he was aware that it would ultimately be destroyed. [Therefore,] he constructed a chamber, in which the ark could be entombed below [the Temple building] in deep, maze-like vaults.
King Josiah commanded that [the Ark] be entombed in the chamber built by Solomon, as it is said (II Chronicles 35:3): "And he said to the Levites who would teach wisdom to all of Israel: 'Place the Holy Ark in the chamber built by Solomon, the son of David, King of Israel. You will no [longer] carry it on your shoulders. Now, serve the Lord, your God.'
When it was entombed, Aharon's staff, the vial of manna, and the oil used for anointing were entombed with it. All these [sacred articles] did not return in the Second Temple.
Similarly, the Urim V'Tumim that existed in the Second Temple did not answer with Ruach HaKodesh (Divine inspiration) and questions were not asked of them, as stated [in Ezra 2:63]: "until a priest will arise with the Urim V'Tumim." [In the Second Temple,] they only made them to fulfill the requirement of eight garments for the High Priest. Thus, the High Priest would not lack one of the required garments.