Replicator cannot interact or influence what happens in an engine. This means that the workflow instances on both the source and target farms perform each configured action fully as they work through the workflow.
If a workflow action creates a task, then Replicator can detect it and not duplicate the work; however, any other actions that a workflow performs on both web applications may be duplicated. Workflow actions include email notifications, the creation of SharePoint objects like list items, or the modification of anything outside of SharePoint.
For example, the generation of email notifications for a workflow occurs entirely within the SharePoint Workflow engine.
Replicator is able to capture and rationalize SharePoint artifacts, such as tasks and column changes, but email notifications occur outside of our scope and are therefore duplicated.
If you are creating custom workflows in SharePoint Designer or Visual Studio, then we recommend creating separate workflows, where one sends an email notification and the other does not. You can also build logic into the workflow to detect where the event originated and only send emails from that farm. Alternatively you can prevent duplication of workflow actions by using ReplicatorAlertFlag - please see this section for more details.
If you are configuring Replicator for disaster recovery, where the Disaster Recovery (DR) farm is quiet until an outage occurs, then we recommend disabling outgoing email from the DR farm. As a part of your fail-over steps, you can enable outgoing emails on that farm, which allows workflow alerts to be sent as expected when the primary farm is unavailable. This prevents SharePoint from sending duplicate alerts from your DR farm.
In the event that you have a workflow that creates list items or documents automatically, Replicator replicates them to both sides, creating duplication of the item. To prevent this from occurring, we recommend that you create your workflow with a unique field. You can then use this unique field to create a rule which will skip replication on the specified unique list item column condition. This rule will prevent the items created by the workflows from being replicated.