you dont have to disconnect both meshes. you could disconnect one mesh, delete the smooth version. and then select both base objets and add shell. now both base meshes belong to the same network. now select them both and do a "merge multiple shells". now they act like one shell. to connect them really, you had to delete the 2 faces between them and you are done. maybe making merging the verts too.

p.s.: you dont have to merge the vertices with cps. if they are at same position it is enough. there will be no seam in the smooth version - as if both shells were one.