More research is needed for this article.
Reason given: Which games did it occur in?
The GTS vanishing glitch was a Global Trade System glitch in Generation IV where the 'Summary' button is replaced with the 'Deposit' button after the player has already submitted a Pokémon.
The glitch could be replicated by simply pressing 'B' on the 'Summary' screen. If the player attempted to deposit a Pokémon when one was already deposited they would receive a communication error and be forced out of the Global Trade System.
This glitch could be temporarily fixed by logging out of the Global Trading System and logging in again, but this did not prevent the glitch from happening again.
This glitch seemingly does not occur in Pokémon X and Y.