I think the same thing happened to me. I did the update and it showed:
Removed entities
high-iron-chest-6 (container) 368
wide iron-chest-6 (container) 96
After reloading and enabling Merging Iron it shows:
Changed entities
wide-iron-chest-6->WideChests_wide-iron-chest-6 96
high-iron-chest-6->WideChests_high-iron-chest-6 368
The chests look fine now. What I don't understand is why I had to turn on iron chests in the first place. My understanding is that my prior setup only allowed me to use iron chests, no other kind. Then when I did the upgrade, it forgot that I had already chosen Iron and made me pick it again.
Anyway, thanks for the fix!