Connected am (أم) coordinates explicit alternatives and helps specify what the questioner seeks to identify. With the hamza, the relevant uncertain constituent is brought into focus.
«أَفِي الْخَابِيَةِ دِبْسٌ أَمْ فِي الزِّقِّ؟»
Is the syrup in the jar or in the wineskin?
The earlier question was about the nature of the contents. This one asks about its location. Neither should be flattened into an undifferentiated yes/no question. The answer must select an alternative that resolves the intended uncertainty.