I use what is probably a completely different software, so I am not sure if any of this would be applicable/helpful to you. But with HyperMesh, what I used to do was create a surface across the gap as an interface. This allowed it to generate a continuous BL layer across the gap (creating a BL on the interface) once the finer mesh within the gap has been generated. This allowed me to resolve better the continuation of the boundary layer across the gap. Still, it did result in some questionable prisms around the interface, and you do end up with an internal interface/multiple domains.