after stopping medication can acid reflux come back again in children

I have a 18 month old boy and he stopped taking medication at 1 year, all symptoms stopped, recently last weekend, he began to throw up and have diarreah, we went to the dr and he said it was simply the seasonal flu, well it has been 6 days and he is still throwing up, usually when he first gets up in the morning is when he vomits, and the diarreah will continue throughout the day, no fever and he is very irratable, doesn't want to be on his back again to get diaper changes... I fear that his reflux is returning and that this is more than just the seasonal flu. If it was flu wouldn't he be throwing up every time he ate throughout the day rather than first thing in the morning after the food has sat on his tummy? I'm one very conscerned mother and I just want to know if anyone out there has been through this?