Some flux height sensing equipment for flux reservoirs require a dye to be added in order to discern the level of a given flux pool. Colored flux can also help with flux deposit inspection, since clear flux deposits are invisible to most optical inspection equipment. These are both great reasons to use a flux that has a distinct color, but my favorite reason seems at first to be a disadvantage to a dyed material.
When you clean up after using a dyed flux, most people mention that it ‘gets all over’ the equipment, and cleaning takes a bit longer. The cleanup is not actually any more difficult, a flux isn’t going to magically migrate to new parts of your machine – you just notice it more than a clear flux (which makes you wonder if you were really cleaning your equipment effectively before). So the real advantage of using a colored flux may be that it teaches your operators how to completely clean flux from equipment – a skill that I think many technicians can improve upon.