Can GERD cause desaturation during daytime, while seated? My 6yo trachee complained of pain in chest during lunch, took sats & 84, hr 125. O2 resolved

Possibly. Acid reflux itself cannot cause problems in the lungs; however, it is possible for someone to aspirate stomach contents, particularly if they have a tracheotomy. If stomach acid is aspirated, it can certainly irritate the lung tissue causing a drop in oxygen sats if the patient begins to breath irregularly.
Possibly. Gerd could cause pain in abdomen or chest even if sitting up, and it could trigger bronchospasm leading to oxygen desaturation. Reflux and an aspiration event could trigger this during eating. A mucus plug could also be the cause of this in a patient with a trach.There are other considerations as well.