It is possible that the player can just start a new game and replay them, or you could make it so that the treasure chests just don't re-contain items, as you are just replaying it.
Another option I thought of is to randomize like, 2 to 4 different chest layouts (Or more if you are crazy), that randomizes each time you do the story. Hear me out.
By layouts, I mean that there are different patterns to where the chests spawn, and this algorithm will make it happen.
Let's say there are 3 chest layouts.
First you'll need to make a variable called "Chest Layout" and randomize it from 1-3. Then you'll need to set up 3 switches called "Layout 1" "Layout 2" and "Layout 3". Then you'll need three more switches called "Different Layout 1" "Different Layout 2" and "Different Layout 3". And that is all you need.
When you enter the story with a new playthrough, check the variable "Chest Layout" to see if it is 1, 2, or 3. If it is 1, activate switches Different Layout "2" and "3". If it is 2, activate switches Different Layout "1" and "3". If it is 3, activate switches Different Layout "1" and "2". Using the order I provided below, it will disable the other layouts, while opening up the randomized layout, making it so that chests will always show up, and it also will add a nice feature to redos.
When you leave the story, remember to randomize the Chest Layout variable, and the rest will work itself, but make sure it doesn't equal what it was before, or else it will glitch, as it won't be able to access Event 5 which resets the chests. Another glitch is if on a previous playthrough you open a chest that is in a room you are not required to enter, then the player does not enter that room on their playthrough, then it will glitch if the layout is the same as the first on their third playthrough if they try to enter the room, since the event didn't reset and activate from them entering the map, since it requires the player to be on the same map to activate. There are no glitches otherwise, since this even works for unopened chests on playthroughs..
This is an exemplar for a layout 1 chest.
Event 1: (Unopened Chest Graphic) (Action Button)
Switch "Layout 1" Required
Gives Item Found
Event 2: (Open Chest Graphic) (Action Button)
Self Switch "A" Required
Does Nothing
Event 3: (No Graphic) (Parallel Process)
Switch "Different Layout 2" Required
Activates Self Switch "B"
Event 4: (No Graphic) (Parallel Process)
Switch "Different Layout 3" Required
Activates Self Switch "B"
Event 5: (No Graphic) (Autorun)
Switch "Layout 1" Required
Self Switch "B" Required
Deactivates Self Switch "A" First
Then Deactivates Self Switch "B" Second
Which will put the whole event back at "Event 1"
I think you can figure out how to change it for when the Layout is 2 or 3, or if you have more layouts. I hope this helps for chests.
Just another thing, you can't use the same variables for different stories, so you'll need to make multiples of each variables.