diff --git a/scripts/update_appup.escript b/scripts/update_appup.escript
index 65be8239b..530f15072 100755
--- a/scripts/update_appup.escript
+++ b/scripts/update_appup.escript
@@ -368,7 +368,12 @@ update_appups(Changes) ->
 do_update_appup(App, Upgrade, Downgrade, OldUpgrade, OldDowngrade) ->
     case locate(src, App, ".appup.src") of
         {ok, AppupFile} ->
-            render_appfile(AppupFile, Upgrade, Downgrade);
+            case contains_contents(AppupFile, Upgrade, Downgrade) of
+                true ->
+                    ok;
+                false ->
+                    render_appfile(AppupFile, Upgrade, Downgrade)
+            end;
         undefined ->
             case create_stub(App) of
                 {ok, AppupFile} ->
@@ -408,6 +413,17 @@ create_stub(App) ->
             false
     end.
 
+%% we check whether the destination file already has the contents we
+%% want to write to avoid writing and losing indentation and comments.
+contains_contents(File, Upgrade, Downgrade) ->
+    %% the file may contain the VSN variable, so it's a script
+    case file:script(File, [{'VSN', 'VSN'}]) of
+        {ok, {_, Upgrade, Downgrade}} ->
+            true;
+        _ ->
+            false
+    end.
+
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %% application and release indexing
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%