Try to use the Transaction.End and Transaction.Start nodes and see if that helps you. Depending on the complexity of the graph and the nodes used you can’t delete an element that isn’t “Committed” to the model yet. Often creating and deleting items in the same run can do this.
It may also help if you share some or all of your graph so we can verify the best way to help you.
You should use Transaction.End after the first part and then use Passthrough or “Await” connect the Transaction.End as wait for and Passtrough the second part.