Interior Flux-BC (as well as 2D-DFE's) are not suitable to model an impervious section inside the model domain (these are only additive terms in the flow equation, setting them to zero would be the same as applying nothing at all).
You can create a gap inside your superelement mesh to prevent flow across it, or apply a very low conductivity (~factor 1000) to this zones (at least two cells wide, otherwise the averaging of the material props can "smear away" these low conductive zones).
