It certainly is possible that some certain things like chest could behave wierdly with moving saves between diffretn versions but it also just could be a bug.
Luckely it's not game breaking in any capacity since getting a duplicate of that item won't do anything.
Most chests in the game work with a non unique switches to save on memory and since it makes more sense programming wise. Which maybe could be affected by saves, in certain cases.
But a lot of the non unique switches are also used in cutscense and major story events and since they do not repeat, I wouldn't be so sure if it has something to do with it.
For now I will keep an eye on the chests.
But I will continue to look further into it.
Thanks for the information.