Communication is a major theme in Serial Experiments Lain, especially in the anime. A major means of communicating is the Wired; many people even think that online communication makes face-to-face communication redundant.
Lain is shown to be extremely isolated at the beginning of the anime, game and manga. Through the anime, she gradually develops friendships - especially with Alice - and connects with people through the Wired. While Eiri tries to tempt her into thinking that reality is unnecessary to her, she learns from Alice and Yasuo that having a physical existence and being able to communicate face-to-face is still important.
Bearing this in mind, the reset takes on an even greater significance - it is the greatest sacrifice made by someone who could only appreciate the value of having a body for a brief time.