ultimately, Pilates is just one modality of many. If the movements traditionally associated with Pilates are just not for that client, then just do something else with the client. Check out MELT with its MELT Strength component, for example, or use balls. There is so much else.
You could try suggesting that the client not eat a full size meal for two hours before doing exercise, and eat the non trigger foods for a preworkout snack one hour before exercise. Then try doing workouts that do not involve lying prone or supine, rather on an incline at most.
I hope this helps you both, good luck.