I think it would very rarely be the best way to solve a problem but if you have to reset a Project.toml file, open it in an editor and remove everything after the first section. This keeps the identity of a package/project but removes all dependencies, etc.
To reset a Manifest.toml file, simply delete it and let Pkg regenerate it. This is a much more useful operation and frequently the best resolution if you have a merge conflict in the Manifest.