This is an issue debated by the Rabbis of the Talmud. Here is what we wrote about it in our Point by Point outlines for Yoma 52b and 53b-54a.

Be well,

Kollel Iyun Hadaf

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Yoma 52b

3) THE KODESH HAKODOSHIM OF THE FIRST MIKDASH

(a) Question: Of which Mikdash is the Mishnah speaking?

1. If the first, there was no Paroches!

2. If the second, there was no Aron (which, the Beraisa

reports, was one of the items hidden by Yoshiyahu)!

i. The Beraisa lists and discusses the items

placed in Genizah by Yoshiyahu.

ii. R. Elazar cites the sources for each of the

items (Tzintzenes, Shemen, Makel).

(b) Answer: We are speaking of the Mikdash Sheini and he came

not to the Aron but to its place.

(c) Question: But the Mishnah speaks of between the Badim?!

(d) Answer: It means as if it were...

Yoma 54

1) WAS THE ARON HIDDEN OR EXILED?

(a) The Mishnah implies that the Aron was exiled.

(b) There are two opinions (R. Eliezer and R. Shimon b.

Yochai) which maintain that it was exiled (based on two

different Pesukim) and one which maintains that it was

hidden in its place, and remains so, based on the words

"Ad ha'Yom ha'Zeh".

1. According to Ula, R. Shimon b. Yochai is of the

opinion that the Aron is hidden.

2. Ula reported an exchange between R. Masia b. Charash

and R. Shimon b. Yochai.

(c) Question: Are all occurrences of "Ad ha'Yom ha'Zeh" meant

to be taken literally?

1. The Pasuk speaks of the Yevusi living in

Yerushalyaim "Ad ha'Yom ha'Zeh".

2. We know from Yirmeyahu that there were 52 years of

total desolation (like the numerical value of

'Beheimah').

3. We also know (from R. Yosi in the Beraisa) that

Gafris and Melach alone reigned in Eretz Yisrael for

seven years (compare "B'ris"-"B'ris").

(d) Answer: The word "Sham" adds the real impression of

forever.

(e) Question: But we find an instance of "va'Yeishev Sham"

which was interrupted by Sancheriv?

(f) Answer: Good question.

2) WHERE WAS THE ARON HIDDEN?

(a) Chachamim (cited by R. Nachman) taught that the Aron is

beneath the wood-checking Lishkah.

(b) A tragic incident reported in the Beraisa supports the

claim that the Aron is not beneath the Kodesh

ha'Kodoshim.

1. In the incident a Kohen, engaged in another

activity, died while trying to point out the place

of the Aron to the other Kohanim.

2. Question: What was that Kohen doing?

3. Answer: He was using his ax (as confirmed by the

tragic incident reported by a Tana d'bei R.

Yishmael).