Any toughness-modifying effects, counters, Auras, or Equipment will apply after its toughness is set to your former life total. For example, say Tree of Redemption is enchanted with Lunarch Mantle (which makes it 2/15) and your life total is 7. After the exchange, Tree of Redemption would be a 2/9 creature (its toughness became 7, which was then modified by Lunarch Mantle) and your life total would be 15.