Here's an character diagram of what such a workflow looks like:
S ↓ D ↓ ↓ MR -> MR ↓ E
I see 3 ways to handle this (please provide ideas if you have any!):
Create a special link that can only exist when importing and give links a color to display relationship.
Create a special link that can be explicitly placed between two nodes (this implies that links will be dragable).
Choose an entirely different representation for our DAG.