It will be a challenge to efficiently implement all of the in-game mechanics, especially to unloaded chunks. My ideas so far are to apply most of the effects once a chunk is reloaded, but I could also queue some changes to be applied later - even reloading the chunk to make some changes.
Could you keep some running score of the entire carbon footprint of the current chunk? Then if the player moved into a new chunk, you would use the old chunk's last score as having some effect on the current chunk?
I guess that wouldn't account for continued tree growth or burning in the chunk you just left though...