Q
An area enchant card was already in set zone C, and I set another area enchant card while preparing for the turn.
Does the effect of the area enchant card that was already out take effect?
A
Generally, no.
If you set a new area enchant card while one is already out, they're swapped at the area enchant swap step after the turn starts. After that, only the newly set area enchant card's effect takes effect, if it can be used.
If an effect's timing is before the card swap, the area enchant card that was already out has its effect resolved, then the cards are swapped, and then the newly set area enchant card's effect is resolved.