Consider a couple basic tests to best mitigate the issue for your schedulers and planners. My opinion if I understand the issue correctly, I believe this falls on posted output and/or posting of the times, likely the ladder.
When you post output, does the order update the allocated time? Easy test here is pick a job, identify the total hours, post half of the output and see if the time reduces in half. If it does, you are likely on the right path on changing setups between serial and parallel, there might be further setup or change to needing to be required.
If they do not, then same test with posting of run time. This should reduce the allocated hours respectively, however, you must do this for all routing lines!
I hope this helps you out additionally with this issue.
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