First thing first, they shouldn't even be there. I don't know why you have so many holes but there should be way less.
BTW I started to use a "new" method for building sidewalks and since then I had no holes at all. I'm using a curbstone spline I made which is standard spline instead of surface spline (so it doesn't screw up the terrain). Also I switch of all the terrain editing in he spline. For the polygon I'm using a polygon with switched off terrain editing functions (height adjust, terrain adjust horizontally and so on). I'm placing the polygon a centimeter under the level of the top of the curbstone, so there is no need of adjusting the polygon to the spline, terrain, etc.
This way nothing is built into the ground (of course it's saved into the terrain though), the terrain is not edited, so it doesn't produce holes either. Also it's faster to build in my opinion.
First thing first
Second thing first:
Use cut meshs, where applicable. While digging for the article I just found out that the topic Cut meshs ("Schneidmeshs" or "Schnittmeshs" in German) is not yet translated. I am going to do this now. But you can use a translator first to get an idea of it: https://www.lotus-simulator.de…s-separaten-Schneidemeshs
Now translated: https://www.lotus-simulator.de…g-splines/#4-Optimization
Thanks for the answers!