Hmm? Nah, depositing it, then counting the clock tics and then turning it off at (hopefully) the exact right time. It makes it so that, while the Pokemon goes onto the GTS, it also rolls back your game save to when you still had the Pokemon in your party. So, since GTS exists in real time, the one that went up stays up.
I clone on Pearl, since it doesn't work on Platinum. They fixed it.