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 Iwakura 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 Mizuki - and connects with people through the Wired. While Masami Eiri tries to tempt her into thinking that reality is unnecessary to her, she learns from Alice and Yasuo Iwakura 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.