I’m not sure I understand the question. As the docs say, Netlify does not support the git clone method of using themes with Hugo, and the better approach is to use git submodule.
Installed this theme https://github.com/JugglerX/hugo-hero-theme using git clone, built project, then subsequently learned Netlify does not support. So am wondering:
any way I can take existing project and modify it so it considers the theme to have been installed using git submodule or;
save my existing project files, start new project by installing theme using git module, then copy `existing project
If you have not made a lot of modifications to your project, and if you are not too comfortable using git, your option #2 is probably the easiest way to do it.