Is it possible to highlight the milestones which have changed after running a Milestones refresh to update my presentation schedule with dates from Microsoft Project?
Yes. On the Milestones Refresh Options dialog box, there is an option Highlight Changed Dates. If this option is checked then when the refresh is done, changed items will be highlighted as shown in the example below.
To turn the highlighting on/off there is a toggle available on the Connections tab on the toolbar.