Almost all of the old mainframe airline reservation system "hosts" have a process for changes to a PNR that allow changes to be done, but that also has a "commit" at the end where everything is confirmed. If that commit (end transaction) fails then the PNR is not modified at all and nothing is changed or lost. I wonder if the agent was creating a new PNR and cancelling the previous and that process had the disappearing inventory and caused the OP pain.

ETA: Alternatively, if the agent incorrectly ended the transaction after cancelling but before rebooking on the same PNR, that would cause this problem as well.