click commands will exit the whole program after being called if 'standalone_mode = False' is not passed. On linux, this ended up not mattering because the file written to by pip_compile is a symlink to the file in the source tree. Symlinks are disabled by default on windows, so it writes to a new file in the runfiles tree but doesn't copy back to the source tree because the program exits.

Author: ChewyGumball

python/private/pypi/dependency_resolver/dependency_resolver.py

@@ -182,7 +182,7 @@ def main(
                         resolved_requirements_file, requirements_file_tree
                     )
                 )
-        cli(argv)
+        cli(argv, standalone_mode = False)
         requirements_file_relative_path = Path(requirements_file_relative)
         content = requirements_file_relative_path.read_text()
         content = content.replace(absolute_path_prefix, "")