Jason
I would guess that it depends on how you are implementing the InfoWindow. The user either closes the InfoWindow/Popup window if they are using that type of implementation or if the infoWindow is hooked up to the AttributeInspector for example then you would simply clear the feature layer selection. For example, I have hooked up the AttributeInspector to a tab container so that the results are displayed in the left panel as opposed to the ESRI InfoWindow. Then I provided the user a button that allows them to clear the selection. In code behind, I call the FeatureLayer.clearSelection method.