Calling of Data.setModified(false) from tests for PHP file doesn't reset state of file opened in editor. It seems that SaveCookie is not removed. Please, reassign if it is not bug in loaders (bug 199990 might be related). It is P2 because it blocks PHP validation tests. To reproduce try the following test case:

public class SetModifiedTest extends NbTestCase {

    public static Test suite() {
        return NbModuleSuite.createConfiguration(SetModifiedTest.class).enableModules(".*").clusters(".*").gui(false).suite();
    }

    public SetModifiedTest(String name) {
        super(name);
    }

    public void test1() throws Exception {
        FileSystem fs = FileUtil.createMemoryFileSystem();
        FileObject f = fs.getRoot().createData("index.php");
        DataObject dob = DataObject.find(f);
        System.out.println("dob=" + dob);
        dob.getLookup().lookup(EditorCookie.class).openDocument().insertString(0, "modified", null);
        assertTrue("Should be modified.", dob.isModified());
        dob.setModified(false);
        assertFalse("Should not be modified.", dob.isModified());
        assertNull("Should not have SaveCookie.", dob.getLookup().lookup(SaveCookie.class));
    }
}