Unfortunately I am not aware of a way to know which students are in progress but it would definitely reset their progress to swap the link out because you are re-directing the current assignment to a new SCORM.
For our setup, we are not publishing the new assignment. We put the updated assignment in a separate assignment group for added clarity. If the new assignment is published and the students have access to the assignments tab in the navigation menu then even if you don't attach it to a module, they would be able to see two separate assignments. If it's a grade assignment, that would also mean both assignments would show in the gradebook.
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