Anticipating the destruction of the Beis Hamikdash, Shlomo Hamelech built winding passageways deep under the Temple floor. Here the Aron would be hidden so that it would never be destroyed or taken captive.
The Aron was absent from the Kodesh Hakodashim in the second Beis Hamikdash, but its presence and influence was there from deep below the surface.
Unlike the rest of the Beis Hamikdash which was completely destroyed and the other Keilim which were plundered, the Aron was untouched by the destruction.
Inside the Aron were the Luchos, with the words of the Aseres Hadibros carved into stone. Unlike written letters, where the ink and paper are ultimately separate, carved letters are one with the stone into which they are cut.
The Aron represents the essence of the Neshama. At the outer levels of our soul, we become connected to Hashem like ink on paper through the Mitzvos that we do, through our feelings and meditation. At our essential core, like the letters on the Luchos, we and Hashem are one.
The destructive forces of our animalistic soul may attack our inner Beis Hamikdash, eroding our outer levels of connection. But deep inside of us and ever present, our Yechida, our essential oneness with Hashem, is untouchable.