diff --git a/reflex/app.py b/reflex/app.py
index c52f0ef8a..4af183367 100644
--- a/reflex/app.py
+++ b/reflex/app.py
@@ -839,6 +839,9 @@ class App(Base):
         compile_results.append(
             compiler.compile_contexts(self.state, self.theme),
         )
+        # Fix #2992 by removing the top-level appearance prop
+        if self.theme is not None:
+            self.theme.appearance = None
 
         app_root = self._app_root(app_wrappers=app_wrappers)
 
diff --git a/reflex/utils/pyi_generator.py b/reflex/utils/pyi_generator.py
index 82eb7cb80..208696979 100644
--- a/reflex/utils/pyi_generator.py
+++ b/reflex/utils/pyi_generator.py
@@ -34,6 +34,7 @@ PWD = Path(".").resolve()
 
 EXCLUDED_FILES = [
     "__init__.py",
+    "app.py",
     "component.py",
     "bare.py",
     "foreach.py",
@@ -795,7 +796,11 @@ class PyiGenerator:
         file_targets = []
         for target in targets:
             target_path = Path(target)
-            if target_path.is_file() and target_path.suffix == ".py":
+            if (
+                target_path.is_file()
+                and target_path.suffix == ".py"
+                and target_path.name not in EXCLUDED_FILES
+            ):
                 file_targets.append(target_path)
                 continue
             if not target_path.is_dir():