Before the swap, Lin Yi first used his ability to Predict Crisis and, seeing that all was calm, he began to call out to his Hua Tuo clone in his mind, "Fellow Daoist Hua Tuo, I'm ready. Are you available for the swap now?"
In reality, he didn't need the consent of his clone to enter it and take over at any moment, while the three Nascent Soul clones would not be able to enter the main body on their own without his command; likewise, they could not swap with each other.
These three clone bodies were all transformed from his Creation Nascent Infant, so naturally, he held ultimate authority over them, entering a clone was the same as entering his own body.
If the distance was close enough, he could enter the clone directly without using anything, but now that the distance was quite far, he needed to rely on his Merciful Title and the Creation Method to accomplish the transfer of his Primordial Spirit.