diff --git a/system/lib/update_libcxx.py b/system/lib/update_libcxx.py
index f8e6ee74c464a..b4557dde0f602 100755
--- a/system/lib/update_libcxx.py
+++ b/system/lib/update_libcxx.py
@@ -34,7 +34,7 @@ def clean_dir(dirname):
   if not os.path.exists(dirname):
     return
   for f in os.listdir(dirname):
-    if f in preserve_files:
+    if f in preserve_files or 'emscripten' in f:
       continue
     full = os.path.join(dirname, f)
     if os.path.isdir(full):
diff --git a/system/lib/update_libcxxabi.py b/system/lib/update_libcxxabi.py
index a939501865563..ad3e75d9e9027 100755
--- a/system/lib/update_libcxxabi.py
+++ b/system/lib/update_libcxxabi.py
@@ -16,12 +16,12 @@
 local_inc = os.path.join(local_root, 'include')
 
 excludes = ('CMakeLists.txt',)
-preserve_files = ()
+preserve_files = ('cxa_exception_js_utils.cpp', '__cpp_exception.S')
 
 
 def clean_dir(dirname):
   for f in os.listdir(dirname):
-    if f in preserve_files:
+    if f in preserve_files or 'emscripten' in f:
       continue
     full = os.path.join(dirname, f)
     if os.path.isdir(full):
diff --git a/system/lib/update_libunwind.py b/system/lib/update_libunwind.py
index f9d4ff8883f77..ad77168d9b59f 100755
--- a/system/lib/update_libunwind.py
+++ b/system/lib/update_libunwind.py
@@ -21,7 +21,7 @@
 
 def clean_dir(dirname):
   for f in os.listdir(dirname):
-    if f in preserve_files:
+    if f in preserve_files or 'emscripten' in f:
       continue
     full = os.path.join(dirname, f)
     if os.path.isdir(full):
diff --git a/system/lib/update_llvm_libc.py b/system/lib/update_llvm_libc.py
index 8508bb792b67b..352ca9e6b23ac 100644
--- a/system/lib/update_llvm_libc.py
+++ b/system/lib/update_llvm_libc.py
@@ -50,7 +50,7 @@ def clean_dir(dirname):
   if not os.path.exists(dirname):
     return
   for f in os.listdir(dirname):
-    if f in preserve_files:
+    if f in preserve_files or 'emscripten' in f:
       continue
     full = os.path.join(dirname, f)
     if os.path.isdir(full):