Chapter 13: Passage to Delphi
1. At the start of the chapter, you have to use the Amulet of Uroburos to partially restore the debris. Jump on the bridge and follow the path as it curves to the left. Here you'll find a decayed chest that you can restore using the amulet.
Delphi Passage Decayed Chest
Chapter 14: The Cistern
2-3. Jump to the lower ground and take out all enemies to unblock the path. You'll find a decayed chest along the way. Restore it and follow the corridor. Turn to the right before reaching the health and magic chests to find another decayed chest.
Cistern Decayed Chests 1 and 2
4-5. Defeat the cyclops and the parasites but before restoring the wooden bridge, head to the right to find another decayed chest. Jump on the lower ground below and you'll find two red chests again inside the house. Proceed further to the right to find yet another decayed chest.
Cistern Decayed Chests 3 and 4
Chapter 16: Prison of the Damned
6. After fixing another large part of the prison, jump off then grapple the massive chains below. Swing across more green objects until you reach a ledge. Follow the stairs down and head to the right to find a decayed chest along the way. Restore it and collect the red orbs then go down the ladder.
Chapter 19: The Foot of Apollo
7. After the chapter starts, climb the wall to the left and make your way up until you reach a ledge. Before continuing to the left, head to the right to find the last decayed chest. Restore it and open it to unlock the trophy “It if Ain't Broke”
Later in the game, you'll come across destroyed later in the game. Once you've obtained the amulet of Uroburos as part of the story, you'll be use its power to restore the chests and collect the red orbs they have within. Finding and restoring all chests will unlock the trophy “If it ain't broke...”