As explained in The Ark King Yoshiahu (Josiah) is supposed to have hidden the Ark and the other items that were with it in secret rooms under the first temple. These were never found during the second temple period and beyond. If the original Torah scroll was placed with the Aron (Ark), then it would be found in the secret chamber when the mashiach comes and the third temple is built.
Tradition records that even as King Solomon built the First Temple, he
already knew, through Divine inspiration, that eventually it would be
destroyed. Thus Solomon, the wisest of all men, oversaw the
construction of a vast system of labyrinths, mazes, chambers and
corridors underneath the Temple Mount complex. He commanded that a
special place be built in the bowels of the earth, where the sacred
vessels of the Temple could be hidden in case of approaching danger.
Midrashic tradition teaches that King Josiah of Israel, who lived
about forty years before the destruction of the First Temple,
commanded the Levites to hide the Ark, together with the original
menorah and several other items1, in this secret hiding place which
Solomon had prepared.
1 such as the staff of Aaron that brought forth almond blossoms during the controversy involving Korach (Numbers 16); the jar of manna that
had been placed in the Holy of Holies as a testimony; and the jar of