diff --git a/src/change_processor.rs b/src/change_processor.rs
index 88e727cb..a0d0518d 100644
--- a/src/change_processor.rs
+++ b/src/change_processor.rs
@@ -657,9 +657,8 @@ impl JobThreadContext {
                                     // If a rename handler already moved the file,
                                     // use the new path instead of the stale
                                     // instigating_source path.
-                                    let effective_path = overridden_source_path
-                                        .as_deref()
-                                        .unwrap_or(path.as_path());
+                                    let effective_path =
+                                        overridden_source_path.as_deref().unwrap_or(path.as_path());
 
                                     if old_is_script && new_is_script && effective_path.exists() {
                                         // Script-to-script transition: rename the file extension.
diff --git a/src/web/api.rs b/src/web/api.rs
index 4c2861b8..969d5a45 100644
--- a/src/web/api.rs
+++ b/src/web/api.rs
@@ -332,6 +332,10 @@ impl ApiService {
         // Process removed instances (syncback: delete files from Rojo filesystem)
         // Phase 1: Gather paths with the tree lock held.
         // Phase 2: Delete files without the lock.
+        // Only IDs that are actually removable (have a Path instigating source)
+        // are included in the PatchSet. ProjectNode instances are skipped so
+        // they are NOT removed from the in-memory tree.
+        let mut actually_removed: Vec<Ref> = Vec::new();
         if !request.removed.is_empty() {
             let removal_actions: Vec<(Ref, Option<(PathBuf, bool)>)> = {
                 let tree = self.serve_session.tree();
@@ -371,6 +375,7 @@ impl ApiService {
                             "Syncback: Path already removed (likely parent was deleted): {}",
                             path.display()
                         );
+                        actually_removed.push(id);
                         continue;
                     }
                     if is_dir {
@@ -384,6 +389,7 @@ impl ApiService {
                             );
                         } else {
                             log::info!("Syncback: Removed directory at {}", path.display());
+                            actually_removed.push(id);
                         }
                     } else {
                         self.suppress_path(&path);
@@ -396,6 +402,7 @@ impl ApiService {
                             );
                         } else {
                             log::info!("Syncback: Removed file at {}", path.display());
+                            actually_removed.push(id);
                         }
                         // Also remove adjacent meta file.
                         // Strip known script suffixes (.server, .client, etc.)
@@ -506,7 +513,7 @@ impl ApiService {
 
         tree_mutation_sender
             .send(PatchSet {
-                removed_instances: request.removed,
+                removed_instances: actually_removed,
                 added_instances: Vec::new(),
                 updated_instances,
             })
diff --git a/tests/tests/two_way_sync.rs b/tests/tests/two_way_sync.rs
index 74c6a631..08157a3c 100644
--- a/tests/tests/two_way_sync.rs
+++ b/tests/tests/two_way_sync.rs
@@ -1154,13 +1154,9 @@ fn get_encoded_names_instance(
 #[test]
 fn add_child_to_encoded_module_creates_encoded_directory() {
     run_serve_test("syncback_encoded_names", |session, _redactions| {
-        let (session_id, encoded_module_id) =
-            get_encoded_names_instance(&session, "What?Module");
+        let (session_id, encoded_module_id) = get_encoded_names_instance(&session, "What?Module");
 
-        let standalone_file = session
-            .path()
-            .join("src")
-            .join("What%QUESTION%Module.luau");
+        let standalone_file = session.path().join("src").join("What%QUESTION%Module.luau");
         // The CORRECT directory name uses the encoded filesystem name
         let encoded_dir = session.path().join("src").join("What%QUESTION%Module");
         // The WRONG directory name would use the decoded instance name
@@ -1231,8 +1227,7 @@ fn add_child_to_encoded_module_creates_encoded_directory() {
 #[test]
 fn add_child_to_encoded_script_strips_suffix_correctly() {
     run_serve_test("syncback_encoded_names", |session, _redactions| {
-        let (session_id, encoded_script_id) =
-            get_encoded_names_instance(&session, "Key:Script");
+        let (session_id, encoded_script_id) = get_encoded_names_instance(&session, "Key:Script");
 
         let standalone_file = session
             .path()
@@ -1304,8 +1299,7 @@ fn add_child_to_encoded_script_strips_suffix_correctly() {
 #[test]
 fn add_child_to_encoded_model_creates_encoded_directory() {
     run_serve_test("syncback_encoded_names", |session, _redactions| {
-        let (session_id, encoded_model_id) =
-            get_encoded_names_instance(&session, "What?Model");
+        let (session_id, encoded_model_id) = get_encoded_names_instance(&session, "What?Model");
 
         let standalone_file = session
             .path()
@@ -1369,21 +1363,14 @@ fn add_child_to_encoded_model_creates_encoded_directory() {
 #[test]
 fn property_update_on_encoded_script_uses_encoded_meta_path() {
     run_serve_test("syncback_encoded_names", |session, _redactions| {
-        let (session_id, encoded_module_id) =
-            get_encoded_names_instance(&session, "What?Module");
+        let (session_id, encoded_module_id) = get_encoded_names_instance(&session, "What?Module");
 
-        let script_file = session
-            .path()
-            .join("src")
-            .join("What%QUESTION%Module.luau");
+        let script_file = session.path().join("src").join("What%QUESTION%Module.luau");
         let encoded_meta = session
             .path()
             .join("src")
             .join("What%QUESTION%Module.meta.json5");
-        let decoded_meta = session
-            .path()
-            .join("src")
-            .join("What?Module.meta.json5");
+        let decoded_meta = session.path().join("src").join("What?Module.meta.json5");
 
         assert_file_exists(&script_file, "Encoded script file before property update");
         assert_not_exists(&encoded_meta, "Meta file before property update");