That is strange, but yeah, my best guess is what you mentioned - that the rest of the reservation got cancelled because the first flight was missed.

Did this happen on Tuesday? If so, and the delay was caused by the SHARES outage, maybe the agents didn't have the ability to properly modify the reservation. Well, technically SHARES was not down, just the "bridge" between SHARES and the airports and the outside world was out, so from the agents' perspective it was all out.