Question:

During the First Temple Era, the Tablets of the Covenant were kept in the Holy of Holies.  Will the Tablets be restored in the Third Temple?

Answer:

The tablets given to Moses by G-d on Mount Sinai were placed in the Ark of the Covenant, which accompanied the Jewish People on all their journeys through the desert.  Once the people reached Israel, the Ark was moved several times until it was brought to its permanent location in the Holy Temple in Jerusalem.

When Solomon built the Temple, he foresaw that it would ultimately be destroyed, and he dug a deep, winding canal under the Ark.  Before the destruction of the Temple, King Josiah had the Ark brought into the hiding place that Solomon had prepared. 

The fact that Solomon built the hiding place for the Ark into the original structure of the Temple indicates that the Ark was not “hidden,” but simply moved from one rightful location to the other.  In other words, from the outset there were two places designated for the Ark.  One, the above-ground location, served the Ark until the destruction, while the second, below ground, was reserved for the time it would be needed.

Naturally, the above-ground, revealed location is preferable.  However, during the exile the Ark is safely in its hiding place deep within the ground, and its holiness is not affected in the slightest.  Therefore, the holiness of the Temple is always present until this day since the Ark was not destroyed, but merely hidden.

When the Third Temple will be rebuilt, speedily in our days, the Ark will be taken out of its hiding place and restored to the Holy of Holies.  Thus, the Third Temple will contain in it an integral part of the First and Second Temples.

Mishna Torah, Hilchot Beit Habechira, chapter 4.  Likutei Sichot vol. 21 p. 156.