If the pictures below you can see the result is acceptable, then do the following.
Open the KML file for editing with Notepad application.
From the "<Folder> <name> Waypoints </ name>" section to "</ coordinates> </ Point> </ Place Market> </ Folder>" section you have to delete all rows. If this is not correct for you, we are looking for a different solution.
I attach the modified KML file.
Spoiler: kml file
Before editing:
After editing:
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