Deletion occurs when an entity comes into contact with the Digital Sea. The DNA and coding of the person that dropped into the digital sea is then dropped by the qubits of the Supercomputer, spreading the DNA and coding for the person virtual shell and physical body across the network into many millions of parts, effectively killing them. It is one of the things most feared by the Lyoko Warriors. Many close calls have been had, with Yumi being the only one who has ever fell into it, in Cruel Dilemma. She was saved by Jeremie's one shot devirtualization program, which relocated, recompiled, and reconstructed Yumi's physical and mental body, at the cost of not being able to devirtualize Aelita yet.
When something falls into the Digital Sea, a beautiful, glowing white column of light emanates from the part of the Digital Sea which the object fell into.
Falling into the Digital Sea would result in the deletion of the subject. The only exceptions to this effect are The Skidbladnir, X.A.N.A.-William, and Franz Hopper. Falling into the celestial dome in the exterior of Carthage would have the same effects as falling into the Digital Sea.
Being devirtualized without the scanners being online would also cause deletion, as the security protocol that regulates forced devirtualization will not be overridden by any command. It will attempt to discharge the quantum memory in use holding the matter and brain activity of the person, and upon realizing a scanner is not connected, it will auto-dump the quibits being used to hold the massive amount of data that the human makeup is. This ensures permanent virtualization.
The only thing so far to have brought back a deleted character is Jeremie's one-shot materialization program, but there is no way that he can rewrite the program, from not knowing the code that was typed in by Odd accidentally dropping candy on the keyboard.
In Distant Memory, Aelita was thrown into the Digital Sea, and the white column of light was seen, meaning that she was deleted. However, Franz Hopper brought her back onto safe land, which may possibly mean that Franz Hopper is able to reconstruct physical bodies after they have fallen into the Digital Sea.