Running the IDE with
 -J-Dorg.openide.text.UndoRedoManager.level=FINE

Rename refactoring of BeanA->protectedProperty (including getters and setters) adds the following edits:

BeanB.java *:URM@627519224->addEdit-atSavepoint: WrapUndoEdit@423407351->UndoableWrapper$UndoableEditDelegate@1594025746
BeansD.java *:URM@1469370668->addEdit-atSavepoint: WrapUndoEdit@1798360223->UndoableWrapper$UndoableEditDelegate@1355420083
BeanA.java *:URM@1152072424->addEdit-atSavepoint: WrapUndoEdit@1168668816->UndoableWrapper$UndoableEditDelegate@931355050
BeanC.java *:URM@82404821->addEdit-atSavepoint: WrapUndoEdit@1998357879->UndoableWrapper$UndoableEditDelegate@1904116920
BeansD.java *:URM@1469370668->addEdit: WrapUndoEdit@78904713->UndoableWrapper$UndoableEditDelegate@1154101192
BeanA.java *:URM@1152072424->addEdit: WrapUndoEdit@1316302281->UndoableWrapper$UndoableEditDelegate@1863389020
BeanC.java *:URM@82404821->addEdit: WrapUndoEdit@1225234939->UndoableWrapper$UndoableEditDelegate@302928690
BeansD.java *:URM@1469370668->addEdit: WrapUndoEdit@2064605899->UndoableWrapper$UndoableEditDelegate@790576267
BeanA.java *:URM@1152072424->addEdit: WrapUndoEdit@2032124293->UndoableWrapper$UndoableEditDelegate@333070563
BeanA.java *:URM@1152072424->addEdit: WrapUndoEdit@1321457162->UndoableWrapper$UndoableEditDelegate@454644460
BeansD.java *:URM@1469370668->    NEW-saveActionsEdit: CompoundEdit@1465629449
BeansD.java *:URM@1469370668->addEdit-performingSaveActions: BaseDocument$AtomicCompoundEdit@2020468078
BeansD.java *:URM@1469370668->    COMPLETED-saveActionsEdit: CompoundEdit@1465629449
BeanC.java *:URM@82404821->    NEW-saveActionsEdit: CompoundEdit@209228324
BeanC.java *:URM@82404821->addEdit-performingSaveActions: BaseDocument$AtomicCompoundEdit@1069711329
BeanC.java *:URM@82404821->    COMPLETED-saveActionsEdit: CompoundEdit@209228324
BeanB.java *:URM@627519224->    NEW-saveActionsEdit: CompoundEdit@356177908
BeanB.java *:URM@627519224->addEdit-performingSaveActions: BaseDocument$AtomicCompoundEdit@1245175567
BeanB.java *:URM@627519224->    COMPLETED-saveActionsEdit: CompoundEdit@356177908
BeanA.java *:URM@1152072424->    NEW-saveActionsEdit: CompoundEdit@1057459996
BeanA.java *:URM@1152072424->addEdit-performingSaveActions: BaseDocument$AtomicCompoundEdit@155490200
BeanA.java *:URM@1152072424->    COMPLETED-saveActionsEdit: CompoundEdit@1057459996

savepoint means a position in UndoManager's queue where the file is either unmodified or at a point where save was performed.
saveActionsEdit(s) above are compound edits produced by performing a save operation
 and they currently only include possible edits produced by Trailing Whitespace Removal operation.

Subsequent Ctrl+Z then does:

BeanA.java *:URM@1152072424->WrapUndoEdit.undo: WrapUndoEdit@1168668816->UndoableWrapper$UndoableEditDelegate@931355050
BeanA.java *:URM@1152072424->beforeUndoAtSavepoint: WrapUndoEdit@1168668816->UndoableWrapper$UndoableEditDelegate@931355050
BeanA.java *:URM@1152072424->    saveActionsEdit.undo(): CompoundEdit@1057459996

What is strange to me is that these actions occur even before the dialog asking whether the refactoring undo should be done or not.

When confirming the dialog then

BeansD.java *:URM@1469370668->WrapUndoEdit.undo: WrapUndoEdit@1798360223->UndoableWrapper$UndoableEditDelegate@1355420083
BeansD.java *:URM@1469370668->beforeUndoAtSavepoint: WrapUndoEdit@1798360223->UndoableWrapper$UndoableEditDelegate@1355420083
BeansD.java *:URM@1469370668->    saveActionsEdit.undo(): CompoundEdit@1465629449
BeansD.java *:URM@1469370668->afterUndoCheck-atSavepoint: WrapUndoEdit@1798360223->UndoableWrapper$UndoableEditDelegate@1355420083

At this point my breakpoint in UndoRedoManager.editToBeUndoneRedone() was hit and so
the edit-to-be-undone is asked for BeansD.java but the UM's queue is empty so null edit is returned.

Then the following is done

BeanA.java *:URM@1152072424->delegateUndoFailedAtSavepoint: WrapUndoEdit@1168668816->UndoableWrapper$UndoableEditDelegate@931355050
BeanA.java *:URM@1152072424->    saveActionsEdit.redo(): CompoundEdit@1057459996

and finally a dialog gets displayed saying

Cannot undo
Following files were modified:
.../BeansD.java

which is IMHO wrong since I did not modify BeansD.java by manual editing.