Geometries with holes are fully-supported in the new LBT 1.3.0 plugin.
The new LBT Honeybee plugin automatically handles the translation of the hole/boundary vertices into a single list of vertices that winds inward to cut out the holes from the shape. So just use the LBT 1.3 plugin for your energy modeling, @SimaKhayami94 , and you won’t experience this issue.