If he has a milk protein allergy/intolerance and is drinking a milk-based formula, not only could that aggravate his reflux but it could upset his tummy and make him not want to eat. You said you tried Nutramigen but did you try Alimentum? The RTF version tastes better and is usually well tolerated, especially if you switch over slowly. Also, is he on meds for his reflux? If not, untreated reflux pain can cause a feeding aversion.