Hi Luke,
I vaguely remember seeing the exact model a while back. Maybe you posted it or somebody else did it. This is kind of a bug or a limitation in Boundary Patch. BP tries to fit a G2 continuous surface on a given loop. Depending on the continuity of the loop, sometimes a G2 surface may not be found. BP could loosen the loop tolerance in order to find the G2 surface, leading to a gap like this.
Instead of creating BP over the loop, I think it is better to restore the base surface. I am not sure if you are aware of a workflow like this.
1) Create a zero offset surface on the thin face.
2) Copy Object -> pick the offset surface -> send it to Repair Environment. The surface will be copied to RE.
3) Edit RE -> Extract Loop -> pick the inner loop of the surface -> check Delete Wires. You will get the untrimmed surface defining the thin surface.
I think this is the surface you need. BP will only complicate geometry in this particular case.
Many thanks!
Johnson Shiue (johnson.shiue@autodesk.com)
Software Test Engineer