It disappeared about the time the Babylonians sacked Jerusalem. It may have been hidden away by the priests of the Temple, but more likely it was taken as part of the loot by the invaders. The odd lack of any mention of it in the Temple literature since then looks like deliberate redaction. Since the Ark was to have made the Israelites invincible in battle, and it did not, that omission can be taken as a political device to support the needs of the ruling class following its restoration by the Persians when they overran Babylon. Their defeat and captivity (it was, after all, only the upper classes that were taken to Babylon, not the commoners) made a strong argument that the Ark's reputation as an artifact of supernatural power in the real world was mythological, and the rulers of Judah, who after Babylon were desperately seeking a way to get back into God's good graces and their own positions of social privilege, wealth and power, would not want to highlight that.
So goes my view of it, at any rate. This perspective is not meant to challenge or offend people who see it differently. YMMV.