diff --git a/commands/make/make.drush.inc b/commands/make/make.drush.inc
index 7ddc41b..cede560 100644
--- a/commands/make/make.drush.inc
+++ b/commands/make/make.drush.inc
@@ -509,7 +509,11 @@ function make_move_build($build_path) {
         // TODO: This only protects one level of directories from being removed.
         $files = drush_scan_directory($file->filename, '/./', array('.', '..'), 0, FALSE);
         foreach ($files as $file) {
-          $ret = $ret && drush_copy_dir($file->filename, $destination . DIRECTORY_SEPARATOR . $file->basename, TRUE);
+          #$ret = $ret && drush_copy_dir($file->filename, $destination . DIRECTORY_SEPARATOR . $file->basename, TRUE);
+          # drush_copy_dir will delete code in existing installs.
+          # http://drupal.org/node/1539076
+          # Extend the $overwrite flag to offer a 'merge' option.
+          $ret = $ret && drush_copy_dir($file->filename, $destination . DIRECTORY_SEPARATOR . $file->basename, 'FILE_EXISTS_MERGE');
         }
       }
       else {
diff --git a/includes/filesystem.inc b/includes/filesystem.inc
index 7b049c4..f00e5dd 100644
--- a/includes/filesystem.inc
+++ b/includes/filesystem.inc
@@ -159,18 +159,25 @@ function drush_delete_tmp_dir($dir) {
  *   it to "d", then $dest = "/c/d".
  * @param $overwrite
  *   If TRUE, the destination will be deleted if it exists.
+ *   If neither TRUE or FALSE, try to merge instead. (needs work)
+ *   http://drupal.org/node/1539076
  * @return
  *   TRUE on success, FALSE on failure.
  */
 function drush_copy_dir($src, $dest, $overwrite = FALSE) {
   // Preflight based on $overwrite if $dest exists.
   if (file_exists($dest)) {
-    if ($overwrite) {
+    if ($overwrite === TRUE) {
       drush_op('drush_delete_dir', $dest, TRUE);
     }
-    else {
+    elseif ($overwrite === FALSE) {
       return drush_set_error('DRUSH_DESTINATION_EXISTS', dt('Destination directory !dest already exists.', array('!dest' => $dest)));
     }
+    elseif ($overwrite == 'FILE_EXISTS_MERGE') {
+      // $overwrite flag may indicate we should merge instead.
+      // That's OK to just continue.
+      drush_log('Merging, not overwriting');
+    }
   }
   // $src readable?
   if (!is_readable($src)) {