I don't think there's an easy way to clear the global undo stack. I don't
think that's a good idea anyway...

For the current operation though you can use set your own UndoContext and
then decide to abort the Undo buffer like this:

try  // Make sure UndoContext gets cleaned up ALWAYS!
{
   this.applicationObject.UndoContext.Open("Insert XML Comment from Help
Builder", false);

   // *** Insert the XML From our Element
   if !this.AddInHelper.InsertXmlComment(Comment, Element)
       this.applicationObject.UndoContext.SetAborted();

}
finally
{
   this.applicationObject.UndoContext.Close();
}

You can set a current UndoContext and then optionally abort it so whatever
you do basically never ends up in the UndoBuffer.

+++ Rick ---

The only way that I can think of to do this is to create your own
custom undo object that implements IOleParentUndoUnit. If you do this,
you can collect the text changes within your object and then you have
complete control over the creation of your object on the redo stack. If
you aren't familiar with this interface, there is great information in
the Platform SDK.