I believe the EPCs use a thermal conductivity reading to measure the flow, so if there is still moisture in the air supply line it will cause the reading to be off just as if you were to try to measure the flow of nitrogen when it EPC is set to be using Helium. You need to flush and dry the supply lines very well, and possibly use a moisture trap just before the instrument until you are sure the lines are completely dry(indicating moisture trap should show when it is dry).
Then recheck and see if there is a difference in measured versus reading for the air flow. If so then I believe it can be recalibrated, but I don't have the procedure for the 7890 on hand for that, but I am sure someone here probably does.