Can't locate /.Spotlight-V100 anywhere, spotlight has incomplete results even after index rebuild
Just tested on a macOS Catalina 10.15.6 system, used the following command in Terminal to remove the .Spotlight-V100 directory:
sudo rm -r /System/Volumes/Data/.Spotlight-V100

It deleted the .Spotlight-V100 directory and in less than a minute recreated it and started indexing the system again.