Fill Dig Holes

You could delete it; that should close the gap. If you look straight down at it, you usually see some tiny shape to move or delete it with.
 
If you cant see the marker in the hole, usually a small square or similar down in the hole which is what you normally click on to delete, then copy a blank bit of board and pasting it over the hole should do it, probably flatten the terrain though.
 
Actually so long as you un-tick terrain/splines/texture on the Copy/Paste tool it should only remove fixed objects in that area.
 
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