Is this reproducible?
Nodes module just reports that the actual Node implementation (FolderNode) fires a property that's not in its property set.
Anyway, it is strange that it happens in this case, FolderNode should actually have the "files" property.
Maybe some race condition in FolderNode - firing a change from incompletely initializes Node?
 

Yes, reproducible today in the log on Build 11020000, XP (Dual processor Sony Vio), 
JDK1.6.0_03. It is a warning and not caught by the exceptions reporter.

from the log:

WARNING [org.netbeans.api.java.source.JavaSource]: JavaSource.runUserActionTask called in AWT event thread by: 
org.netbeans.modules.web.struts.StrutsConfigUtilities.getActionServlet(StrutsConfigUtilities.java:257)
java.lang.IllegalStateException: Warning - the node "resourcesnoderenamed" [org.openide.loaders.DataFolder$FolderNode] 
is trying to fire the property files which is not included in its property sets. This is illegal. See IZ #31413 for 
details.
        at org.openide.nodes.Node.firePropertyChange(Node.java:929)
        at org.openide.loaders.DataNode.access$900(DataNode.java:61)
        at org.openide.loaders.DataNode$4.run(DataNode.java:706)
        at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
        at java.awt.EventQueue.dispatchEvent(EventQueue.java:597)
        at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:273)
        at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:183)
        at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:177)
        at java.awt.Dialog$1.run(Dialog.java:1039)
        at java.awt.Dialog$3.run(Dialog.java:1091)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.awt.Dialog.show(Dialog.java:1089)
        at org.netbeans.core.windows.services.NbPresenter.superShow(NbPresenter.java:834)
        at org.netbeans.core.windows.services.NbPresenter.doShow(NbPresenter.java:868)
        at org.netbeans.core.windows.services.NbPresenter.run(NbPresenter.java:856)
        at org.netbeans.core.windows.services.NbPresenter.run(NbPresenter.java:104)
        at org.openide.util.Mutex.doEventAccess(Mutex.java:1223)
        at org.openide.util.Mutex.readAccess(Mutex.java:242)
        at org.netbeans.core.windows.services.NbPresenter.show(NbPresenter.java:841)
        at java.awt.Component.show(Component.java:1419)
        at java.awt.Component.setVisible(Component.java:1372)
        at java.awt.Window.setVisible(Window.java:801)
        at java.awt.Dialog.setVisible(Dialog.java:979)
        at org.netbeans.modules.refactoring.spi.impl.ParametersPanel.showDialog(ParametersPanel.java:505)
        at org.netbeans.modules.refactoring.spi.impl.RefactoringPanel.refresh(RefactoringPanel.java:605)
        at org.netbeans.modules.refactoring.spi.impl.RefactoringPanel.<init>(RefactoringPanel.java:139)
        at org.netbeans.modules.refactoring.spi.impl.RefactoringPanel.<init>(RefactoringPanel.java:131)
        at org.netbeans.modules.refactoring.spi.ui.UI.openRefactoringUI(UI.java:72)
        at org.netbeans.modules.refactoring.java.ui.RefactoringActionsProvider$NodeToFileObjectTask.run
(RefactoringActionsProvider.java:684)
        at org.netbeans.modules.refactoring.java.RetoucheUtils.invokeAfterScanFinished(RetoucheUtils.java:900)
        at org.netbeans.modules.refactoring.java.ui.RefactoringActionsProvider.doRename
(RefactoringActionsProvider.java:156)
        at org.netbeans.modules.refactoring.api.impl.ActionsImplementationFactory.doRename
(ActionsImplementationFactory.java:69)
        at org.netbeans.modules.refactoring.spi.impl.RenameAction.performAction(RenameAction.java:62)
        at org.netbeans.modules.refactoring.spi.impl.RefactoringGlobalAction.performAction
(RefactoringGlobalAction.java:131)
        at org.openide.util.actions.NodeAction.performAction(NodeAction.java:289)
        at org.openide.util.actions.CallableSystemAction$1.run(CallableSystemAction.java:118)
        at org.netbeans.modules.openide.util.ActionsBridge.doPerformAction(ActionsBridge.java:77)
        at org.openide.util.actions.CallableSystemAction.actionPerformed(CallableSystemAction.java:114)
        at org.openide.util.actions.NodeAction.actionPerformed(NodeAction.java:277)
        at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995)
        at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318)
        at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
        at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
        at javax.swing.AbstractButton.doClick(AbstractButton.java:357)
        at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1216)
        at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1257)
        at java.awt.Component.processMouseEvent(Component.java:6038)
        at javax.swing.JComponent.processMouseEvent(JComponent.java:3265)
        at java.awt.Component.processEvent(Component.java:5803)
        at java.awt.Container.processEvent(Container.java:2058)
        at java.awt.Component.dispatchEventImpl(Component.java:4410)
        at java.awt.Container.dispatchEventImpl(Container.java:2116)
        at java.awt.Component.dispatchEvent(Component.java:4240)
        at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4322)
        at java.awt.LightweightDispatcher.processMouseEvent(Container.java:3986)
        at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3916)
        at java.awt.Container.dispatchEventImpl(Container.java:2102)
        at java.awt.Window.dispatchEventImpl(Window.java:2429)
        at java.awt.Component.dispatchEvent(Component.java:4240)
        at java.awt.EventQueue.dispatchEvent(EventQueue.java:599)
        at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:273)
        at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:183)
        at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:173)
        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:168)
        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:160)
        at java.awt.EventDispatchThread.run(EventDispatchThread.java:121)

IDE:-------------------------------------------------
IDE: [4.11.07 12:02] Committing "DataFolderTest.java" started
Checking in DataFolderTest.java;
/cvs/openide/loaders/test/unit/src/org/openide/loaders/DataFolderTest.java,v  <--  DataFolderTest.java
new revision: 1.13; previous revision: 1.12
done
IDE: [4.11.07 12:02] Committing "DataFolderTest.java" finished

The test seems to work and I cannot reproduce in IDE. All I got is 

java.lang.NullPointerException
	at org.netbeans.modules.web.jspparser.JspParserImpl.initReflection(JspParserImpl.java:101)
	at org.netbeans.modules.web.jspparser.JspParserImpl.createParseProxy(JspParserImpl.java:198)
	at org.netbeans.modules.web.jspparser.JspParserImpl.getParseProxy(JspParserImpl.java:189)
	at org.netbeans.modules.web.jspparser.JspParserImpl.getJspOpenInfo(JspParserImpl.java:145)
	at org.netbeans.modules.web.core.jsploader.TagLibParseSupport.getCachedOpenInfo(TagLibParseSupport.java:269)
	at 
org.netbeans.modules.visualweb.project.jsfloader.JsfJspDataObject.updateFileEncoding(JsfJspDataObject.java:312)
	at 
org.netbeans.modules.visualweb.project.jsfloader.JsfJspDataObject.getFileEncoding(JsfJspDataObject.java:300)
	at org.netbeans.modules.visualweb.project.jsfloader.JsfJspDataObject$1.getEncoding(JsfJspDataObject.java:137)
	at 
org.netbeans.modules.openide.loaders.DataObjectEncodingQueryImplementation.getEncoding(DataObjectEncodingQueryImplementation.java:86)
	at org.netbeans.api.queries.FileEncodingQuery.getEncoding(FileEncodingQuery.java:93)

Sorry. Provide exact steps to reproduce and keep in mind that I do not know how to use VisualWeb.

Steps to reproduce:
1. File->New Project->(category) Web (Projects:) WebApplication, press Next, take default for project name and 
selecting glassfish and ee5 from dropdowns, press Next, check "Visual Web JavaServer Faces" (go with 
the defaults) -> press Finish.
2. In projects window, rename WebApplicationXX/WebPages/resources to anything. Check rename comments and press refactor.
>Will get ISE to the log shortly, or at the start of the next action.

Reproduced in trunk NetBeans IDE Dev (Build 200712141200), 1.6.0_04, XP.

Reproduced with described scenario.

The problem is in firing the property "files" which belongs to DataNode.
But this property is not in list of properties that described by
property sheets.
The exception is thrown for avoiding such situation ( that is described 
above shortly and in IZ##31413 with more details ).
This is "notification" exception for developer like assertion.

I don't know why it is not thrown in refactoring process for java packages 
f.e. Need investigate.

*** Issue 120693 has been marked as a duplicate of this issue. ***

changeset:   73786:036fe5534931