A flashback is a sudden, involuntary memory, often of a violent or painful event. Bourne has flashbacks throughout the novel. For example, he experiences one while thinking about war and waiting to talk to General Villiers.
"Why should these old withered men provoke such feelings of fear and guilt…and loathing?
They were war. They were death. On the ground and from the skies. From the skies…from the skies. Help me, Marie. For God's sake, help me! (25.2-3)
Bourne doesn't know this, but we later find out that he's reliving the death of his wife and son, who were killed by a rogue aircraft in Cambodia.
Within the book, Bourne's flashbacks are presented as a result of his amnesia. Particular sights or sounds or ideas dredge up memories, which he then experiences painfully and involuntarily.
These days, we often think of flashbacks as something that happens to people like returning veterans, especially when they've returned from Vietnam, and with Post Traumatic Stress Syndrome, or PTSD.
Bourne himself, besides being an amnesiac, is also a veteran of the Vietnam War. The returning memories he has (like that of his son's death) are often returning memories of combat or trauma.
Throughout the novel, Bourne remembers things with exaggerated pain. Sometimes, when he tries to remember something, he'll keeps shouting things like: "Oh Christ! Stop it!" (3.101). This freak-outery might make more sense if it's a result of trauma, something like PTSD.
Flashbacks, of course, are also a literary device used to flesh out things happening in the present by backing them up with information from the past. It's interesting that the flashbacks we get here show how traumatize Bourne has been by violence. In some ways, that sort of takes the wind out of the novel's heroic sails: if violence is this bad, then what is going on between Bourne and Carlos can't be all that good.
How do you think this novel really feels about violence? Does it glorify it, or are things more complicated than that?