"Covering Up" ? Do you mean the 1x1 dighole is not present, and the tunnel mouth is filled with a gray 10m x 10m baseboard grid square ?
Tug up and down on the tunnel spline points, and position the tunnel spline points to the center of a 10m x 10m baseboard grid ... Apply a 1x1 dighole ... set "terrain" to minimum radius, and tug up, and down, on the 4 corners of the tunnel mouth 1x1 dighole.