diff --git a/scripts/stability/compare-baseline.js b/scripts/stability/compare-baseline.js
index 45515e6..63cf570 100644
--- a/scripts/stability/compare-baseline.js
+++ b/scripts/stability/compare-baseline.js
@@ -88,7 +88,14 @@ function removeNodeModulesLink(worktreePath) {
     return;
   }
   if (stats.isSymbolicLink()) {
-    fs.rmdirSync(linkPath);
+    // symlinkSync only honours the 'junction' type on Windows. Elsewhere the
+    // link is a plain symlink, which rmdirSync rejects with ENOTDIR; unlinkSync
+    // removes the link itself and likewise never touches the target.
+    if (process.platform === 'win32') {
+      fs.rmdirSync(linkPath);
+    } else {
+      fs.unlinkSync(linkPath);
+    }
   }
 }
 
@@ -222,4 +229,8 @@ function main() {
   console.log(`\nStability comparison complete: ${outputPath}`);
 }
 
-main();
+if (require.main === module) {
+  main();
+}
+
+module.exports = { removeNodeModulesLink };
diff --git a/test/compareBaseline.removeNodeModulesLink.test.js b/test/compareBaseline.removeNodeModulesLink.test.js
new file mode 100644
index 0000000..99366ce
--- /dev/null
+++ b/test/compareBaseline.removeNodeModulesLink.test.js
@@ -0,0 +1,63 @@
+/**
+ * @jest-environment node
+ *
+ * compare-baseline links the main repo's node_modules into each stability
+ * worktree and must detach that link before removing the worktree, without
+ * ever deleting the main repo's real dependencies through it.
+ *
+ * Runs on the real filesystem: the global memfs mock has no Windows junctions,
+ * so it would reject the rmdir that a real junction accepts.
+ */
+
+jest.unmock('fs');
+jest.unmock('fs/promises');
+jest.unmock('os');
+
+const fs = require('fs');
+const os = require('os');
+const path = require('path');
+const { removeNodeModulesLink } = require('../scripts/stability/compare-baseline');
+
+describe('compare-baseline removeNodeModulesLink', () => {
+  let root;
+
+  beforeEach(() => {
+    root = fs.mkdtempSync(path.join(os.tmpdir(), 'stability-link-'));
+  });
+
+  afterEach(() => {
+    fs.rmSync(root, { recursive: true, force: true });
+  });
+
+  test('removes the linked node_modules and leaves its target intact', () => {
+    const mainModules = path.join(root, 'main', 'node_modules');
+    fs.mkdirSync(path.join(mainModules, 'jest'), { recursive: true });
+    fs.writeFileSync(path.join(mainModules, 'jest', 'package.json'), '{}');
+    const worktree = path.join(root, 'worktree');
+    fs.mkdirSync(worktree);
+    // Same call as ensureWorktreeDependencies: a junction on Windows, a plain
+    // symlink elsewhere.
+    fs.symlinkSync(mainModules, path.join(worktree, 'node_modules'), 'junction');
+
+    removeNodeModulesLink(worktree);
+
+    expect(fs.existsSync(path.join(worktree, 'node_modules'))).toBe(false);
+    expect(fs.existsSync(path.join(mainModules, 'jest', 'package.json'))).toBe(true);
+  });
+
+  test('leaves a real node_modules directory alone', () => {
+    const worktree = path.join(root, 'worktree');
+    fs.mkdirSync(path.join(worktree, 'node_modules', 'pkg'), { recursive: true });
+
+    removeNodeModulesLink(worktree);
+
+    expect(fs.existsSync(path.join(worktree, 'node_modules', 'pkg'))).toBe(true);
+  });
+
+  test('does nothing when the worktree has no node_modules', () => {
+    const worktree = path.join(root, 'worktree');
+    fs.mkdirSync(worktree);
+
+    expect(() => removeNodeModulesLink(worktree)).not.toThrow();
+  });
+});