diff --git a/crates/webcodex-cli/src/webcodex_cli/project.rs b/crates/webcodex-cli/src/webcodex_cli/project.rs
index 9d8ad989..a8372ba4 100644
--- a/crates/webcodex-cli/src/webcodex_cli/project.rs
+++ b/crates/webcodex-cli/src/webcodex_cli/project.rs
@@ -57,10 +57,9 @@ fn effective_canonical_roots(
     configured: &[PathBuf],
     allow_cwd_anywhere: bool,
 ) -> Result<Vec<PathBuf>, String> {
-    webcodex_runner_config::effective_allowed_roots(configured, allow_cwd_anywhere)?
-        .into_iter()
-        .map(|root| canonical_existing_directory(&root, "allowed root"))
-        .collect()
+    let effective =
+        webcodex_runner_config::effective_allowed_roots(configured, allow_cwd_anywhere)?;
+    Ok(webcodex_runner_config::paths::canonicalize_usable_allowed_roots(&effective))
 }
 
 fn validate_project_authority(
@@ -406,6 +405,131 @@ mod tests {
         assert!(!registry.exists());
     }
 
+    #[test]
+    fn stale_first_root_does_not_block_later_matching_root() {
+        let tmp = tempfile::tempdir().unwrap();
+        let stale = tmp.path().join("deleted-project");
+        let root = tmp.path().join("root");
+        let project = root.join("demo");
+        let registry = tmp.path().join("registry");
+        std::fs::create_dir_all(&project).unwrap();
+        let config_path = tmp.path().join("runner.toml");
+        config_with_policy(&config_path, &registry, &[stale, root.clone()], false);
+
+        let output = run_project_register(ProjectRegisterOptions {
+            config: config_path,
+            project,
+            json: true,
+        })
+        .expect("a stale unrelated root must not block a later matching root");
+        let output: serde_json::Value = serde_json::from_str(&output).unwrap();
+        assert_eq!(output["project"]["already_registered"], false);
+        assert_eq!(
+            output["policy"]["allowed_roots"],
+            serde_json::json!([root.canonicalize().unwrap().to_string_lossy().to_string()])
+        );
+        assert!(registry.join("demo.toml").is_file());
+    }
+
+    #[test]
+    fn stale_root_and_valid_nonmatching_root_remain_denied() {
+        let tmp = tempfile::tempdir().unwrap();
+        let stale = tmp.path().join("deleted-project");
+        let allowed = tmp.path().join("allowed");
+        let project = tmp.path().join("outside");
+        let registry = tmp.path().join("registry");
+        std::fs::create_dir_all(&allowed).unwrap();
+        std::fs::create_dir_all(&project).unwrap();
+        let config_path = tmp.path().join("runner.toml");
+        config_with_policy(&config_path, &registry, &[stale, allowed], false);
+
+        let error = run_project_register(ProjectRegisterOptions {
+            config: config_path,
+            project,
+            json: false,
+        })
+        .unwrap_err();
+        assert!(error.contains("outside allowed_roots"), "{error}");
+        assert!(!registry.exists());
+    }
+
+    #[test]
+    fn all_stale_roots_remain_denied() {
+        let tmp = tempfile::tempdir().unwrap();
+        let project = tmp.path().join("project");
+        let registry = tmp.path().join("registry");
+        std::fs::create_dir_all(&project).unwrap();
+        let config_path = tmp.path().join("runner.toml");
+        config_with_policy(
+            &config_path,
+            &registry,
+            &[
+                tmp.path().join("deleted-one"),
+                tmp.path().join("deleted-two"),
+            ],
+            false,
+        );
+
+        let error = run_project_register(ProjectRegisterOptions {
+            config: config_path,
+            project,
+            json: false,
+        })
+        .unwrap_err();
+        assert!(error.contains("outside allowed_roots"), "{error}");
+        assert!(error.contains("allow_cwd_anywhere is false"), "{error}");
+        assert!(!registry.exists());
+    }
+
+    #[cfg(unix)]
+    #[test]
+    fn project_symlink_escape_remains_denied() {
+        let tmp = tempfile::tempdir().unwrap();
+        let root = tmp.path().join("root");
+        let outside = tmp.path().join("outside");
+        let registry = tmp.path().join("registry");
+        std::fs::create_dir_all(&root).unwrap();
+        std::fs::create_dir_all(&outside).unwrap();
+        let escape = root.join("escape");
+        std::os::unix::fs::symlink(&outside, &escape).unwrap();
+        let config_path = tmp.path().join("runner.toml");
+        config(&config_path, &registry, &root);
+
+        let error = run_project_register(ProjectRegisterOptions {
+            config: config_path,
+            project: escape,
+            json: false,
+        })
+        .unwrap_err();
+        assert!(error.contains("outside allowed_roots"), "{error}");
+        assert!(!registry.exists());
+    }
+
+    #[test]
+    fn stale_roots_do_not_relax_allow_cwd_anywhere_false() {
+        let tmp = tempfile::tempdir().unwrap();
+        let project = tmp.path().join("ordinary-project");
+        std::fs::create_dir_all(&project).unwrap();
+        let stale = tmp.path().join("deleted-project");
+
+        let denied_registry = tmp.path().join("denied-registry");
+        let denied = register_existing_project(
+            &denied_registry,
+            &project,
+            std::slice::from_ref(&stale),
+            false,
+            None,
+        )
+        .unwrap_err();
+        assert!(denied.contains("allow_cwd_anywhere is false"), "{denied}");
+        assert!(!denied_registry.exists());
+
+        let allowed_registry = tmp.path().join("allowed-registry");
+        register_existing_project(&allowed_registry, &project, &[stale], true, None)
+            .expect("the existing allow_cwd_anywhere relaxation must remain unchanged");
+        assert!(allowed_registry.join("ordinary-project.toml").is_file());
+    }
+
     #[cfg(windows)]
     #[test]
     fn raw_unc_is_rejected_before_canonicalization_even_when_explicitly_allowed() {
diff --git a/crates/webcodex-runner-config/src/paths.rs b/crates/webcodex-runner-config/src/paths.rs
index e5c909f2..c2debad9 100644
--- a/crates/webcodex-runner-config/src/paths.rs
+++ b/crates/webcodex-runner-config/src/paths.rs
@@ -386,6 +386,23 @@ fn is_windows_drive_root(_canonical_path: &Path) -> bool {
     false
 }
 
+/// Canonicalize the `allowed_roots` entries that can currently provide path
+/// authority.
+///
+/// `allowed_roots` is an OR-set of independent authority candidates. A stale,
+/// unmounted, unreadable, non-directory, or otherwise unresolvable candidate
+/// cannot authorize anything, but it must not poison another usable root.
+/// Callers still apply the authoritative path policy after this projection;
+/// an empty result therefore remains fail-closed unless that policy explicitly
+/// permits the target through `allow_cwd_anywhere`.
+pub fn canonicalize_usable_allowed_roots(roots: &[PathBuf]) -> Vec<PathBuf> {
+    roots
+        .iter()
+        .filter_map(|root| root.canonicalize().ok())
+        .filter(|root| root.is_dir())
+        .collect()
+}
+
 /// Authoritative pure path-policy check for Runner project registration.
 ///
 /// `canonical_path` and `canonical_allowed_roots` must already be canonicalized
diff --git a/crates/webcodex-runner/src/webcodex_runner/projects.rs b/crates/webcodex-runner/src/webcodex_runner/projects.rs
index 482e7f88..078c340c 100644
--- a/crates/webcodex-runner/src/webcodex_runner/projects.rs
+++ b/crates/webcodex-runner/src/webcodex_runner/projects.rs
@@ -889,11 +889,8 @@ pub(crate) fn validate_project_path_policy(
     policy: &RunnerPolicy,
     canonical_path: &Path,
 ) -> Result<(), String> {
-    let canonical_roots = policy
-        .allowed_roots
-        .iter()
-        .filter_map(|root| canonicalize_existing(root).ok())
-        .collect::<Vec<_>>();
+    let canonical_roots =
+        webcodex_runner_config::paths::canonicalize_usable_allowed_roots(&policy.allowed_roots);
     webcodex_runner_config::paths::validate_project_path_policy(
         canonical_path,
         &canonical_roots,