Reference Value will effect on the next calculations like Nusselt number so that if you let length as default, this will give you a wrong number. Hence you have to double check the diameter of the bubble if you try to calculate Nusselt number. Good Luck
In my opinion , do not change Reference values first. I want to know, why are you thinking to change these values ? Did you get any divergence or wrong simulations ?
Actually, i read in some forums that these values affect the drag force calculation, but it seems they do not do anything with the drag force between phases as interface force.
Moreover, do you know how we can monitor drag force coefficient (Cd) calculated by a model ( for example the Grace model) in the FLUENT?