Let me rephrase that. The two inputs need to be referenced to the common of the power supply feeding the COM of the AI-110.
If the voltage across the shunt is isolated from GND, you should be able to do it with the one channel.
I mentioned the two channel because you asked about a differential measurement. Depending on the wiring and circuitry involved, a differential measurement can be made by using two single ended inputs and taking the difference of the two measurements. This can be done when the common of the circuit being measured can be tied to the common of the cFP-AI-110 and the two individual input voltages don't exceed the maximum in spec. This allows other measurements that are referenced to the same common to be made on the other channels of the module.