This issue is caused by not following the correct procedure when changing the FactoryMaster (FM) route of an existing works order.
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Once works orders and their associated tasks are imported into Orchestrate, the route in FM shouldn't be changed. If, for any reason, the route needs to be changed, the tasks must be deleted from Orchestrate before importing new tasks (from FM to Orch) based on a different route.
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We cannot change the way the integration works in any other fashion without affecting the core system.

If you would like more details, please chat to support, and we will be happy to explain further.