diff --git a/crates/ruff_db/src/files.rs b/crates/ruff_db/src/files.rs
index 1c322419e0..b58b802faf 100644
--- a/crates/ruff_db/src/files.rs
+++ b/crates/ruff_db/src/files.rs
@@ -526,7 +526,7 @@ impl VirtualFile {
     }
 
     /// Increments the revision of the underlying [`File`].
-    fn sync(&self, db: &mut dyn Db) {
+    pub fn sync(&self, db: &mut dyn Db) {
         let file = self.0;
         tracing::debug!("Updating the revision of `{}`", file.path(db));
         let current_revision = file.revision(db);
diff --git a/crates/ty_server/src/session.rs b/crates/ty_server/src/session.rs
index a5139b714a..bf27411947 100644
--- a/crates/ty_server/src/session.rs
+++ b/crates/ty_server/src/session.rs
@@ -1575,6 +1575,9 @@ impl DocumentHandle {
                         {
                             db.project().remove_file(db, file);
                         }
+
+                        // Bump the file's revision back to using the file system's revision.
+                        file.sync(db);
                     } else {
                         // This can only fail when the path is a directory or it doesn't exists but the
                         // file should exists for this handler in this branch. This is because every
@@ -1598,6 +1601,8 @@ impl DocumentHandle {
                     if let Some(virtual_file) = db.files().try_virtual_file(virtual_path) {
                         db.project().close_file(db, virtual_file.file());
                         virtual_file.close(db);
+                        // Bump the file's revision back to using the file system's revision.
+                        virtual_file.sync(db);
                     } else {
                         tracing::warn!("Salsa virtual file does not exists for {}", virtual_path);
                     }
diff --git a/crates/ty_server/tests/e2e/semantic_tokens.rs b/crates/ty_server/tests/e2e/semantic_tokens.rs
index 5eb5957666..090a1213b8 100644
--- a/crates/ty_server/tests/e2e/semantic_tokens.rs
+++ b/crates/ty_server/tests/e2e/semantic_tokens.rs
@@ -70,3 +70,40 @@ fn multiline_token_client_supporting_multiline_tokens() -> Result<()> {
 
     Ok(())
 }
+
+// Regression test for https://github.com/astral-sh/ty/issues/2346
+#[test]
+fn no_stale_tokens_after_opening_the_same_file_with_new_content() -> Result<()> {
+    let file_name = "src/foo";
+    let initial_content =
+        "def calculate_sum(a):\n # Version A: Basic math\n return a\n\nresult = calculate_sum(5)\n";
+    let mut server = TestServerBuilder::new()?
+        .enable_pull_diagnostics(true)
+        .enable_multiline_token_support(true)
+        .with_workspace(SystemPath::new("src"), None)?
+        .with_file(file_name, initial_content)?
+        .build()
+        .wait_until_workspaces_are_initialized();
+
+    server.open_text_document(file_name, initial_content, 0);
+
+    let initial_tokens = server
+        .semantic_tokens_full_request(&server.file_uri(file_name))
+        .unwrap();
+
+    server.close_text_document(file_name);
+
+    server.open_text_document(
+        file_name,
+        "# Version B: Basic greeting\ndef say_hello():\n print(\"Hello, World!\")\n\nsay_hello()\n",
+        0,
+    );
+
+    let new_tokens = server
+        .semantic_tokens_full_request(&server.file_uri(file_name))
+        .unwrap();
+
+    assert_ne!(initial_tokens, new_tokens);
+
+    Ok(())
+}