Q. If someone suffers from reflux sometimes hours after finishing a meal, can he still say the brocho achrono then?

A. Shulchan Aruch (O.H. 184: 5) rules that one should recite Birchas Hamozon until the food he consumed has been digested and his is now hungry to eat more. Magen Avraham (ibid. 9) and Mishna Berura, (ibid. 20), Kaf Hachaim (ibid. 28) and many others maintain that this normally takes seventy-two minutes. Poskim opine that if he is not hungry yet he can still recite until six hours after eating (Hilchos Ketanos, Chaye Adam 145, Yavetz in Mor Uketzia ibid., Otzar Halochos (p.479 n. 42 etc,)
Horav Shlomo Miller’s Shlit”a opinion is that the reflux is not necessarily the regurgitation of the undigested food still in the stomach. It could be that the reflux is constituted of only acidic leftover fluids left after the digestion. (A medical opinion supported by Dr. Shorser and others) In that case it would depend on whether the person is already hungry again or no. When not clear or in doubt one should maintain the seventy-two minutes as the rule.

Rabbi A. Bartfeld as revised by Horav Shlomo Miller Shlit”a