If you are using snapshot download, all rows in the remote database are deleted before the snapshot is downloaded. If you are using timestamp-based download, you can decide how you want deletes on the consolidated database to be handled on the remote database.
If you want to delete rows from remote databases when they are deleted from the consolidated database, you need to keep a record of the row in order to delete it. You can do this with shadow tables or by using logical deletes.
In Model mode, open the Mappings tab.
In the Table Mappings pane, select a remote table.
In the Download Deletes dropdown list, select the checkbox if you want to download deletes from the consolidated database. Clear the checkbox if you do not want to download deletes from the consolidated database.
If you chose to download deletes, open the Download Deletes tab in the lower pane.
To record deletions, you can choose to use a shadow table or logical deletes.