In Iron Man 3, all of Stark's autonomous suits were destroyed in the helicopter attack, how then did they reappear again in the end?
They were not all destroyed in the helicopter attack. The only suits we saw destroyed at that time were the Marks One through Seven, which had a prominent display above the vault containing the other suits. The vault remained apparently undamaged, so the remaining suits (which we can assume consisted of the Marks Eight through Forty-One) were able to join Stark and Rhodes in Miami once the debris covering the vault was cleared.
If memory serves the suits were in some kind of vault underneath his house. The house fell into the sea but, the vault was still there.