Hey @Asisnath ,
I do not have an easy means of separating the infiltration from the ventilation loads when using the AFN but I am pretty sure that the “AFN Infiltration” is the sum of both infiltration and ventilation. So your charts should still be balanced when using the AFN.
Until E+ supports better AFN outputs, it looks like the only way to separate infiltration from ventilation is by requesting surface-level AFN flow rates and checking whether the flow is from a window. But even that workflow might mix some of the infiltration of closed windows with the ventilation of open windows and you still have to do some heat balance math yourself with the indoor vs. outdoor air temperatures.