Index: library/Zend/View/Helper/HeadScript.php
===================================================================
--- library/Zend/View/Helper/HeadScript.php	(revision 24628)
+++ library/Zend/View/Helper/HeadScript.php	(working copy)
@@ -245,7 +245,7 @@
                     break;
                 case 'file':
                 default:
-                    if (!$this->_isDuplicate($content)) {
+                    if (!$this->_isDuplicate($content) || $action=='set') {
                         $attrs['src'] = $content;
                         $item = $this->createData($type, $attrs);
                         if ('offsetSet' == $action) {
Index: tests/Zend/View/Helper/HeadScriptTest.php
===================================================================
--- tests/Zend/View/Helper/HeadScriptTest.php	(revision 24628)
+++ tests/Zend/View/Helper/HeadScriptTest.php	(working copy)
@@ -451,6 +451,20 @@
 
         $this->assertEquals($expected, $test);
     }
+    
+    /**
+     * @group ZF-12048
+     */
+    public function testSetFileStillOverwritesExistingFilesWhenItsADuplicate()
+    {
+        $this->helper->appendFile('foo.js');
+        $this->helper->appendFile('bar.js');
+        $this->helper->setFile('foo.js');
+        
+        $expected = '<script type="text/javascript" src="foo.js"></script>';
+        $test = $this->helper->toString();
+        $this->assertEquals($expected, $test);
+    }
 }
 
 // Call Zend_View_Helper_HeadScriptTest::main() if this source file is executed directly.