and the Ark is constantly accompanied by clouds: When God spoke from between the Cherubs, there was a glowing cloud visible there
Shemot - Exodus - Chapter 40
35 Moses could not enter the Tent of Meeting because the cloud rested upon it and the glory of the Lord filled the Mishkan.
When the High Priest entered presence of the Ark on Yom Kippur, he did so only under the cover of a cloud of incense, perhaps intended to mask the sight of the shekhina in all its glory.
Vayikra - Leviticus - Chapter 16
13 And he shall place the incense upon the fire, before the Lord, so that the cloud of the incense shall envelope the ark cover that is over the [tablets of] Testimony, so that he shall not die.
G-d Said unto the Prophet Nathan in
Shmuel II - II Samuel - Chapter 7
4 And it came to pass on the same night, that the word of God was to Nathan saying:
5 "Go and say to My servant, to David; so says the Lord: 'Shall you build Me a house for My dwelling
6 For I have not dwelt in a house from the day that I brought up the children of Israel out of Egypt, to this day, but have walked in a tent and in a tabernacle.
7 In all [the places] wherein I have walked with all the children of Israel, did I speak a word with any of the rulers of Israel whom I commanded to shepherd my people Israel, saying: 'Why do you not build for me a house of cedar?'
8 And now, so shall you say to My servant, to David; 'Thus says the Lord of Hosts. I took you from the sheep cote, from following the sheep, to be a leader over My people Israel.
9 And I have been with you wherever you have gone, and I have cut off all your enemies from before you, and have made for you a great name, like the name of the great ones that are in the earth.
10 And I will appoint a place for My people, for Israel, and I will plant them, and they will dwell in their own place, and be disturbed no more; and the wicked people shall not continue to afflict them as formerly.
I can go on, and have a habit of being pithy! LOL So I’ll continue to make my point. The relationship of the Shekhinah, Ark of the Covenant, and the Holy of Holies can readily be seen.
The Ark of the Covenant was lost during the destruction of the first Temple (586 BCE) and never found, although there is a lot of published articles that says that the Ark of the Covenant was hidden in a massive tunnel complex under the Temple Mount, some have claimed that it was found, and it’s location is secret.
The accession of Cyrus the Great of the Persian Empire in 559 BCE made the re-establishment of the city of Jerusalem and the rebuilding of the Temple possible. Construction of the second Temple started 521 BCE under Darius the Great. Ezra - Chapter 5 and was completed during the sixth year of his reign (c. 516 BCE), with the temple dedication taking place the following year.
The events take place in the second half of the 5th century BCE. Listed together with the Book of Ezra as Ezra-Nehemiah, it represents the final chapter in the historical narrative of the Hebrew Bible.
The original core of the book, the first-person memoir, may have been combined with the core of the Book of Ezra around 400 BCE. Further editing probably continued into the Hellenistic era.
Since some of the original artifacts were, according to the biblical account, lost after the destruction of the First Temple, the Second Temple lacked the following holy articles:
In the Second Temple, the Kodesh Hakodashim (Holy of Holies) was separated by curtains rather than a wall as in the First Temple. Still, as in the Tabernacle, the Second Temple included:
According to the Mishnah (Middot iii. 6), the "Foundation Stone" stood where the Ark used to be, and the High Priest put his censer on it on Yom Kippur.
The Second Temple also included many of the original vessels of gold that had been taken by the Babylonians but restored by Cyrus the Great. According to the Babylonian Talmud (Yoma 22b), however, the Temple lacked the Shekinah, the dwelling or settling divine presence of God, and the Ruach HaKodesh, the Spirit of Holiness, present in the first.
I don’t believe that the Devine Presence has ever left the Temple Mount! Because it is said in
Divrei Hayamim II - II Chronicles - Chapter 7
16 And now, I have chosen and consecrated this House that My name be there forever, and My eyes and heart will be there at all times.
Rashi’s commentary
and My eyes and heart will be: Jonathan renders (I Kings 9:3): “and My presence will rest there if My will is performed there at all times.” My eyes will be there if My heart and My will are there.
17 As for you, if you walk before Me as your father David walked, and do according to all that I commanded you, and you keep My statutes and My ordinances.
18 I shall set up the throne of your kingdom as I decreed to your father David, saying: You shall never lack a man ruling in Israel.
I found another source that says that the Shekinah never left.
Permanent Reminder of God's Presence
The Sages prophesied that after the Temple's destruction, the Divine Presence will never leave the Western Wall. For this reason, the Wall will never be destroyed. The Wall is endowed with everlasting sanctity. The Talmud (Megillah 3:3) says: "And I will make your sanctuaries desolate" (Leviticus 26:31) - this means that the sanctuaries retain their sanctity even when they are desolate. (See "Mystical Secret of the Western Wall")
The Wall is therefore a symbol of the Jewish People: Just as there have been many efforts to destroy the Wall - and yet it remains eternal, so too the Jewish People have outlived its enemies and remain eternal!