diff --git a/core/SCsub b/core/SCsub
index 445249a5c00..de2ff26f935 100644
--- a/core/SCsub
+++ b/core/SCsub
@@ -151,6 +151,7 @@ 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/editor/SCsub b/editor/SCsub
index 8ac411dd4e6..9c99f6fa44e 100644
--- a/editor/SCsub
+++ b/editor/SCsub
@@ -91,6 +91,7 @@ if env["tools"]:
     env.CommandNoCache("#editor/builtin_fonts.gen.h", flist, run_in_subprocess(editor_builders.make_fonts_header))
 
     env.add_source_files(env.editor_sources, "*.cpp")
+    env.add_source_files(env.editor_sources, "register_exporters.gen.cpp")
 
     SConscript("collada/SCsub")
     SConscript("doc/SCsub")
diff --git a/main/SCsub b/main/SCsub
index dd1b30eca90..473c1574671 100644
--- a/main/SCsub
+++ b/main/SCsub
@@ -10,18 +10,15 @@ env.main_sources = []
 env.add_source_files(env.main_sources, "*.cpp")
 
 # Order matters here. Higher index controller database files write on top of lower index database files.
-controller_databases = ["#main/gamecontrollerdb.txt", "#main/godotcontrollerdb.txt"]
+controller_databases = ["gamecontrollerdb.txt", "godotcontrollerdb.txt"]
 
-env.Depends("#main/default_controller_mappings.gen.cpp", controller_databases)
-env.CommandNoCache(
-    "#main/default_controller_mappings.gen.cpp",
+gensource = env.CommandNoCache(
+    "default_controller_mappings.gen.cpp",
     controller_databases,
     run_in_subprocess(main_builders.make_default_controller_mappings),
 )
 
-# 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.main_sources, "#main/default_controller_mappings.gen.cpp", warn_duplicates=False)
+env.add_source_files(env.main_sources, gensource)
 
 env.Depends("#main/splash.gen.h", "#main/splash.png")
 env.CommandNoCache("#main/splash.gen.h", "#main/splash.png", run_in_subprocess(main_builders.make_splash))
diff --git a/methods.py b/methods.py
index 047892d813b..9b8cb38c0c1 100644
--- a/methods.py
+++ b/methods.py
@@ -11,7 +11,7 @@ from SCons.Script import Glob
 from SCons.Variables.BoolVariable import _text2bool
 
 
-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 isbasestring(files):
         # Keep SCons project-absolute path as they are (no wildcard support)
@@ -21,17 +21,20 @@ 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)