Depending on the geometry of the hole, a Slanted Wall could be added that fills the hole, then a Window placed in that wall. An image of the shell and hole would help to describe your particular issue.
Create two shells, one as glass, one opaque.
Cut out the opaque shell.
Drop the glass shell down [or in, or whatever] a fraction to avoid OpenGL material flashing.
"The Shell hole is created by an editable cutting body. The cutting body is visible when you select the hole itself, not the Shell.
Once you click the cutting body it will appear the floating menu and then you select Edit extrusion lenght. Just grab it to zero and the hole will be deleted.