Can't remove node_modules folder with symlink

Thank you for your report! It is reproducible; we check all files for read-only status before removing the directory, and we are not aware if something is a symlink.
Here's an issue about it: https://youtrack.jetbrains.com/issue/IDEA-276034/Refactoring-helper-incorrectly-flags-symlinks-pointing-to-non-writable-files-was-Deleting-symlink-directories-is-broken