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If the doctor found irregularities in the childs GI system I am sure he biopsy them, a lot of this is probably of no clinical significance. I wouldn't worry about it, but I think you should discuss your concerns with her doctor, so you can understand exactly what is going on.
There is no clinical data to verify this but several people have reported of the development of stomach irregularies such as; polyps after using Prevacid (tx for GERD) for a while, but as I said this is only reported cases and not actual research or clinical data to prove or disprove. The polyps are usually benign and of no clinical significance.
After an endoscopy has been done it is highly unlikely Gastric cancer is mistaken as GERD or vice versa.