Thanks for your question. If you took the sodium bicarbonate at mealtime — while eating your food — then it certainly would ruin digestion. That’s why, as I’ve said, you should take SB and water 1/2 to 1 hour after you have finished your meal. Main stage digestion occurs in the duodenum — not the stomach. There are some protease enzymes involved with initiating just protein digestion in the stomach and that’s all — but the main digestion of carbohydrates, fats, proteins etc occurs in the duodenum or upper intestines — not the stomach.
In a normal healthy gut, the usefulness of stomach digestion finishes about 20 minutes after you have stopped eating your food, so taking SB and water 1/2 hr to 1 hour after eating accounts for this and will then act to create the right alkaline medium for proper main stage digestion to occur in the duodenum. The reason I give a range of times — 1/2 hr to 1 hour after meals — is to accommodate people with slow digestion which can also be caused by candida, GERD, reflux problems etc.