Instances from an existing workflow schedule will fail with the error "Item reference not found" if a new workflow version is deployed with new item references.
An existing workflow schedule is configured and running. The workflow used in the schedule is updated with new item references and a new version of the workflow is deployed. The existing schedule continues to run and start instances, but these instances go into an error state on the newly added reference step.
Current product functionality requires that if you update and deploy a new version of a workflow that includes changes to item references, any workflow schedules for the process must also be re-created to reflect the changes.