Best way to amend automate enrollments and assignment rules on compliance courses

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We had some compliance courses with reassignment rules set up for us a few years ago. Staff are required to completed the courses based on their job role. Learners were enrolled in 3 different ways:

1. Learners who had completed the training on another platform had their legacy details loaded via 2 separate learning initiatives.
2. Existing staff without a training record were bulk enrolled as a required learning assignment.
3. New employees joining after a specific date are enrolled via a 3rd learning initiative.

Generally, the set up has worked, but we've come across a few issues: