You can simply delete those lines in the configure.bat - that call is downloading and unzipping the files in that directory. If you have already found, downloaded, and unzipped the files (and properly installed protobuf), then you're good to go.
If when you try to compile any other packages, they don't find the dependencies, you can add their path locations in the configure.bat files by adding them to the cmake line here: -DCMAKE_PREFIX_PATH="C:/gz-ws/protobuf-3.4.1-vs19", along with anything else it can't find.