Something similar happened to me 6 months ago.
Party of three , JFK-CDG-SEZ , J , paid. When checked in at JFK , they said we had to get the boarding passes to SEZ in Paris. Once we got in Paris , we tried to get BPs at the self kiosk , but reservation was non existent. We had to find an agent , who confirmed that the tickets miraculously disappeared . Thankfully it took 10 min and two phone calls for the agent to get it fixed.