After you've retrieved all items and you purchased them from the Well Keeper, Treasure Chests become redundant.
I believe you should think of a way to reward the player for discarding the treasure chest's loot some other way.
Here are some suggestions:
- Add items that you can only find from chest (meh?)
or - Allow us to upgrade a selected equipped item to Tier 2 (this sounds fun and like the best option, but requires more work, that is to add a second tier to each item. This option could be unlocked through a new rescued NPC)
or - Give the player XP and/or Gold and/or Full HP heal and/or Revive charge or a Bonus Trait (free lvlup) if he gives up on the treasure.
I love the current mechanic of unlocking gear and being able to gear up however you want in your subsequent runs, but turns out it makes treasure chests redundant once you have everything unlocked.