You're just misunderstanding your TDEE then. It's basic thermodynamics that is very accurate in human digestion too, save for extremes like bulemia, gastric distress (you shit out undigested food), or pills that simulate it w/ carb/fat blockers.
The most pedantic detail is CICO is actually on digested calories, not swallowed calories.
Your anecdata is likely accounted by:
1. Protein takes more calories to digest (many people unintentionally eat more protein on keto, though keto is actually about fat intake and protein can break ketosis through gluconeogensis)
2. Up regulation in things like thermogenesis (ie you lose more calories to the ambient air)
3. Inaccuracy in food tracking
4. Higher NEAT
5. Loss of water weight due to lower food mass in digestive tract, and lower glycogen(+bound water) weight.