Average flux is the average ...

Average flux is the average flux that the membranes see across the entire system.  Depending on array design, membrane type, recovery, feed water chemistry, system design, etc the flux in the stages can be different than the overall average flux.  In reality each membrane is operating at a different flux with the lead elements being the highest and the tail being the lowest.  Projection software will give you warnings if you exceed recommended stage, lead element, or average flux.