diff --git a/core/SCsub b/core/SCsub
index 14dfa3487f..c12dd4e60e 100644
--- a/core/SCsub
+++ b/core/SCsub
@@ -146,6 +146,7 @@ env.core_sources += thirdparty_obj
 # Godot source files
 
 env.add_source_files(env.core_sources, "*.cpp")
+env.add_source_files(env.core_sources, "script_encryption_key.gen.cpp")
 
 # Certificates
 env.Depends(
diff --git a/core/input/SCsub b/core/input/SCsub
index 740398b266..b12bf561de 100644
--- a/core/input/SCsub
+++ b/core/input/SCsub
@@ -7,19 +7,15 @@ import input_builders
 
 # Order matters here. Higher index controller database files write on top of lower index database files.
 controller_databases = [
-    "#core/input/gamecontrollerdb.txt",
-    "#core/input/godotcontrollerdb.txt",
+    "gamecontrollerdb.txt",
+    "godotcontrollerdb.txt",
 ]
 
-env.Depends("#core/input/default_controller_mappings.gen.cpp", controller_databases)
-env.CommandNoCache(
-    "#core/input/default_controller_mappings.gen.cpp",
+gensource = env.CommandNoCache(
+    "default_controller_mappings.gen.cpp",
     controller_databases,
     env.Run(input_builders.make_default_controller_mappings, "Generating default controller mappings."),
 )
 
 env.add_source_files(env.core_sources, "*.cpp")
-
-# Don't warn about duplicate entry here, we need it registered manually for first build,
-# even if later builds will pick it up twice due to above *.cpp globbing.
-env.add_source_files(env.core_sources, "#core/input/default_controller_mappings.gen.cpp", warn_duplicates=False)
+env.add_source_files(env.core_sources, gensource)
diff --git a/editor/SCsub b/editor/SCsub
index d149cc6273..e8d417319a 100644
--- a/editor/SCsub
+++ b/editor/SCsub
@@ -101,6 +101,7 @@ if env["tools"]:
     )
 
     env.add_source_files(env.editor_sources, "*.cpp")
+    env.add_source_files(env.editor_sources, "register_exporters.gen.cpp")
 
     SConscript("debugger/SCsub")
     SConscript("fileserver/SCsub")
diff --git a/methods.py b/methods.py
index 0e71adb40d..428405fb04 100644
--- a/methods.py
+++ b/methods.py
@@ -14,7 +14,7 @@ from SCons.Variables.BoolVariable import _text2bool
 from platform_methods import run_in_subprocess
 
 
-def add_source_files(self, sources, files, warn_duplicates=True):
+def add_source_files(self, sources, files):
     # Convert string to list of absolute paths (including expanding wildcard)
     if isinstance(files, (str, bytes)):
         # Keep SCons project-absolute path as they are (no wildcard support)
@@ -24,17 +24,20 @@ def add_source_files(self, sources, files, warn_duplicates=True):
                 return
             files = [files]
         else:
+            # Exclude .gen.cpp files from globbing, to avoid including obsolete ones.
+            # They should instead be added manually.
+            skip_gen_cpp = "*" in files
             dir_path = self.Dir(".").abspath
             files = sorted(glob.glob(dir_path + "/" + files))
+            if skip_gen_cpp:
+                files = [f for f in files if not f.endswith(".gen.cpp")]
 
     # Add each path as compiled Object following environment (self) configuration
     for path in files:
         obj = self.Object(path)
         if obj in sources:
-            if warn_duplicates:
-                print('WARNING: Object "{}" already included in environment sources.'.format(obj))
-            else:
-                continue
+            print('WARNING: Object "{}" already included in environment sources.'.format(obj))
+            continue
         sources.append(obj)