When the computer scrubs a mission on the pad (by a last-minute countdown failure, for example), it deletes the hardware.
Similarly, when part A of a Joint mission fails before part B launches (e.g., DM or LM doesn't make it into orbit), the game deletes the hardware for part B.
I think both of these happen because the game deletes a mission's hardware prior to launch, possibly as soon as you give last-minute authorization to proceed with the launch.