The missable commendations are:
Chest of Sorrow
Tales of Eternal Sorrow
Pieces of Silver
I have included a brief text description, but if you want the full descriptions with pictures, then I suggest using the excellent guide links provided. I like these guides because they aren't full walkthroughs, so you can still experience the Tall Tale.
Pieces of Silver:Full link - https://rarethief.com/the-sunken-pearl-tall-tale-journals-lo...The first two journals are in the spire part (the tall room with the puzzles), and the last three are in the Citadel.
1. A Run of Good Luck - Behind some wood on the ground floor of the spire room
2. An Ancient Mystery - Near some red rocks on the East side of the tall spire room after it is filled with water
3. Unwanted Company - On the left side of a ship split in two after you open the big citadel doors
4. From Bad to Worse - After swimming through some more tunnels, there will be another shipwreck piece with the next journal on it
5. Don't Look for Us - In a room that will require using a pully to travel upwards in a C-shaped wood piece, There will also be half of a ship that is the Captain Quarter's room holding the last journal in it
Chest of Sorrow and Tales of Eternal Sorrow:Full link - https://rarethief.com/how-to-do-the-tale-of-eternal-sorrow-c...1. Get the Silver Blade ship key
In the same room the last journal was in, we will need to get the Silver Blade key to unlock the door holding the Chest of Sorrow. After you do all the pulley stuff to get across, there is a path left and a path right. You need to go left to a carved face in the wall with red plants in the mouth and a faint red light. The key is through there.
2. Get the Chest of Sorrow
In the next room after continuing on, there will be a big ship: The Silver Blade. Guess where you need to use the key? When you open the door, take the Chest of Sorrow out of the room ASAP and put it near the mast. This is important because you can get locked out of that room after some shenanigans.
3. Bring the Chest of Sorrow to a pink tentacle door
After all the shenanigans are over, take the Chest of Sorrow up the mast ladder and swim out until you reach a room that has some bolder stepping stones on the right side leading to a pink tentacle door. Leave the Chest of Sorrows in front of it, and wait. After it opens, read the etchings on the wall and you are all done with the missable commendations!