Deletions should appear in the manifest summary. To achieve this, the format of the summary records should probably change to something like:
<staged-model class-name="..." added="3" deleted="1"/>
To accommodate the prepare phase, deletions should also be added to the portlet data context (into ManifestSummary) while performing the prepare counts. An easy way to do this is to generate the necessary logic into *ExportActionableDynamicQuery classes.