Atlassian’s migration assistant supports Server/Data Center to Cloud and Cloud to Data Center migrations.
Atlassian does not provide a mechanism for apps like JSU to hook in for a cloud-to-cloud migration. Therefore, JSU does not have an option to officially support such functionality. JSU workflow rules migrated from one cloud instance to another would retain the same IDs for the components they reference from the source instance, which would not be recognized in the destination cloud environment.